[gmx-users] Query regarding the addition of solvent molecule

Justin Lemkul jalemkul at vt.edu
Thu Sep 11 14:52:43 CEST 2014

On 9/11/14 8:49 AM, Christina Florina wrote:
> Hi,
>       [ molecules ]
> ; Compound                 #mols
> Protein_chain_A               1
> CHX                            3414
>           Here no water molecules to replace but to neutralize the system I
> need to replace the solvent ions. As you told I went through the tutorial
> regarding the genion and addition of ions, but to neutralize solvents apart
> from water(SOL) I couldnt find enough details. I tried with methanol, then
> I got Group 13 (MeOH) (instead of SOL) to replace the solvents with the
> ions in the genion step. But with the solvents I am using like cyclohexane,
> I am getting only 9 groups and if I try to choose any group its showing
> error as follows:
>      *Your solvent group size (23449) is not a multiple of 8*
>           I don't know how to resolve this error though I have modified the
> topology file (.top) with the no. of ions. Kindly need help with this
> issue. I have attached the screenshot of the error page in the link below.
> https://www.dropbox.com/sh/vkvsr3u2hmh2ft9/AABxNv6VxA1gbSs7h2gkaIfxa?dl=0

The contents of ions.tpr do not appear to have CHX added.  Note that "Protein" 
and "System" have the same size.  Replacing CHX with ions is just like any other 
solvent (whether or not free ions would exist in a nonpolar solvent like this is 
another issue altogether).  You would choose CHX for replacement.  I suspect the 
.tpr file was constructed incorrectly or the topology is otherwise incorrect in 
its contents.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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