[gmx-users] Regarding No more replaceable solvent!
Dilip H N
cy16f01.dilip at nitk.edu.in
Mon Feb 19 08:35:19 CET 2018
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
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
Then how do i solve this issue..??
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On Mon, Feb 19, 2018 at 11:49 AM, Alex <nedomacho at gmail.com> wrote:
> 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.
> On 2/18/2018 11:14 PM, Dilip H N wrote:
>> 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
>> 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
>> 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
>> 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
>> Any suggestions are appreciated...
>> Thank you
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