[gmx-users] adding SR2++ to charm27 force field

Ming Tang m21.tang at qut.edu.au
Fri Apr 17 03:58:57 CEST 2015

Hi, Justin

Thanks a lot.
Garbage in, garbage out. I should follow logic.

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: Friday, 17 April 2015 11:34 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] adding SR2++ to charm27 force field

On 4/16/15 9:30 PM, Ming Tang wrote:
> Hi, Justin
> I changed "CL" in my pdb file into "CLA". It can be add ions to equilibrate the charge of the system using the modified charmm27.ff. however, when minimising it, I came across an error like this:
> Command line:
>    mdrun -s em.tpr -deffnm em -v
> Back Off! I just backed up em.log to ./#em.log.1# Reading file em.tpr, 
> VERSION 5.0.4 (single precision) Using 1 MPI thread Using 8 OpenMP 
> threads
> Back Off! I just backed up em.trr to ./#em.trr.1#
> Back Off! I just backed up em.edr to ./#em.edr.1#
> Low-Memory BFGS Minimizer:
>     Tolerance (Fmax)   =  1.00000e+00
>     Number of steps    =        50000
> Using 10 BFGS correction steps.
>     F-max             =          inf on atom 30262
>     F-Norm            =         -nan
> Segmentation fault (core dumped)
> tm at tm-HP-Z420-Workstation:~/bmp2$
> I searched the mailing list, and found that you said that there is something catastrophically wrong with the input structure. But, it can be minimised using the original charm27 force field in Gromacs when I consider the ion as MG and CAL.
> Does this mean that there is something wrong with my modified charmm27.ff?

Yes, exactly as I said - you're mixing force field parameters with OPLS Sr2+ and you get a nonsensical physical model.  Garbage in, garbage out.

You need to derive suitable Sr2+ parameters in a manner consistent with the parent force field.  For CHARMM ions, this would involve hydration free energies, QM water interactions, assessing coordination geometry, perhaps specific interactions with carboxylate and/or phosphate, etc.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul

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