[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
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.




‌
<https://mailtrack.io/> Sent with Mailtrack
<https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality>

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.
>
> Alex
>
>
> On 2/18/2018 11:14 PM, Dilip H N wrote:
>
>> 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
>>
>>
>>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student


More information about the gromacs.org_gmx-users mailing list