[gmx-users] Regarding No more replaceable solvent!

[Dilip H N]

Hello,
I added 10 Na+ and Cl- ions to the aminoacid-water system containing 512
molecules through the command
gmx genion -s em.tpr -o abc.gro -p topol.top -pname NA -nname CL -np 10 -nn
10

but now, i want to increase the concentration, so i want to add 45 Na+ and
Cl- ions (from calculation, the concentration for 45 ions is 5M...), but
when i give the commands:
gmx genion -s em.tpr -o glywi.gro -p topol.top -pname NA -nname CL -np 45
-nn 45
(or)
gmx genion -s em.tpr -o glywi.gro -p topol.top -pname NA -nname CL -conc 5

I am getting the error as:

No more replaceable solvent!

So, Is there any limit here..?? The maximum concentration that i can get is
2M (through -conc 2 command), and after that, if i change from -conc2 to
-conc3 etc., i am getting the same error as "No more replaceable solvent!".

Any suggestions are appreciated...

Thank you
--
With Best Regards,

DILIP.H.N
Ph.D. Student



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[Alex]

How about you actually open your 'glywi.gro' prior to adding more ions
and count the number of water molecules, and then compare it with the
number of ions you want to add? With concentration known and the
knowledge of your box volume, this comparison shouldn't be a problem.

Alex

Post by Dilip H N
Hello,
I added 10 Na+ and Cl- ions to the aminoacid-water system containing 512
molecules through the command
gmx genion -s em.tpr -o abc.gro -p topol.top -pname NA -nname CL -np 10 -nn
10
but now, i want to increase the concentration, so i want to add 45 Na+ and
Cl- ions (from calculation, the concentration for 45 ions is 5M...), but
gmx genion -s em.tpr -o glywi.gro -p topol.top -pname NA -nname CL -np 45
-nn 45
(or)
gmx genion -s em.tpr -o glywi.gro -p topol.top -pname NA -nname CL -conc 5
No more replaceable solvent!
So, Is there any limit here..?? The maximum concentration that i can get is
2M (through -conc 2 command), and after that, if i change from -conc2 to
-conc3 etc., i am getting the same error as "No more replaceable solvent!".
Any suggestions are appreciated...
Thank you

[Dilip H N]

I have a system of 1aminoacid+511 water molecules (total is 512
molecules).and the box length is 2.52nm.

So, even if i replace by 45 Na+ and 45 Cl- ions (total is 90 ions) and
still i have 511-90 = 421 water molecules. and i think this is well within
the solubility...

How many water molecules are being removed for each ion..?? (when i
replaced 10Na+ and 10Cl- ions ie., 511-20=491 water molecules were there
and this system was being well, but now with 45 ions each, i am getting the
error...)

Then how do i solve this issue..??

Any suggestions.

Thank you.




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How about you actually open your 'glywi.gro' prior to adding more ions and
count the number of water molecules, and then compare it with the number of
ions you want to add? With concentration known and the knowledge of your
box volume, this comparison shouldn't be a problem.
Alex

Post by Dilip H N
Hello,
I added 10 Na+ and Cl- ions to the aminoacid-water system containing 512
molecules through the command
gmx genion -s em.tpr -o abc.gro -p topol.top -pname NA -nname CL -np 10 -nn
10
but now, i want to increase the concentration, so i want to add 45 Na+ and
Cl- ions (from calculation, the concentration for 45 ions is 5M...), but
gmx genion -s em.tpr -o glywi.gro -p topol.top -pname NA -nname CL -np 45
-nn 45
(or)
gmx genion -s em.tpr -o glywi.gro -p topol.top -pname NA -nname CL -conc 5
No more replaceable solvent!
So, Is there any limit here..?? The maximum concentration that i can get is
2M (through -conc 2 command), and after that, if i change from -conc2 to
-conc3 etc., i am getting the same error as "No more replaceable solvent!".
Any suggestions are appreciated...
Thank you

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With Best Regards,

DILIP.H.N
Ph.D Student

[Alex]

Please be kind to respond to the list and not to my email. I believe
that 3-4 water molecules get removed per ion, depending on the insertion
cutoff, so with 90 x 4, you're left in a situation where there's pretty
much no water left. Gromacs is actually doing you a huge favor with this
error, because it could manage to insert all the ions and you would end
up simulating something nonsensical.

Increase your box size appropriately.

Alex

Sir,
In connection with the above-mentioned title...
I have a system of 1glycine+511 water molecules (total is 512
molecules).and the box length is 2.51nm.
So, even if i replace by 45 Na+ and 45 Cl- ions (total is 90 ions) and
still i have 511-90 = 421 water molecules. and i think this is well
within the solubility...
Then how do i solve this issue..??
Any suggestions sir.
Thank you.
--
With Best Regards,
DILIP.H.N
Ph.D. Student
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[Dilip H N]

Thank you sir...
Yes, I will post it in the group...




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Please be kind to respond to the list and not to my email. I believe that
3-4 water molecules get removed per ion, depending on the insertion cutoff,
so with 90 x 4, you're left in a situation where there's pretty much no
water left. Gromacs is actually doing you a huge favor with this error,
because it could manage to insert all the ions and you would end up
simulating something nonsensical.
Increase your box size appropriately.
Alex

Sir,
In connection with the above-mentioned title...
I have a system of 1glycine+511 water molecules (total is 512
molecules).and the box length is 2.51nm.
So, even if i replace by 45 Na+ and 45 Cl- ions (total is 90 ions) and
still i have 511-90 = 421 water molecules. and i think this is well within
the solubility...
Then how do i solve this issue..??
Any suggestions sir.
Thank you.
--
With Best Regards,
DILIP.H.N
Ph.D. Student
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With Best Regards,

DILIP.H.N
Ph.D Student