[gmx-users] Gromos54a8

rajat desikan rajatdesikan at gmail.com
Thu Oct 24 15:00:49 CEST 2013

Hi Justin,
Thanks for the comments.

Since the script was written in 2009, I don't want to use it until I verify
that the formats are unchanged.

"The same would apply here - if you want to validate between the two
software packages, carry out equivalent calculations in both programs."

I didn't realize this. I do not have access to gromos software. I was
thinking of reproducing the results in the 54A8 paper using gromacs. But
this seems to be a critical step!

Anyone in the user forum with access to gromos and interested in porting
54A8 to gromacs??

On Thu, Oct 24, 2013 at 6:01 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 10/24/13 6:43 AM, rajat desikan wrote:
>> Dear all,
>> I want to use the Gromos54A8 FF in gromacs. They are available in gromos
>> format in http://www.gromos.net/main.pl   ATB is yet to release it in
>> gromacs format.
>> I want to undertake the conversion of this FF to gromacs format. Apart
>> from
>> ConvertGromos2Gromacs.tgz<http**://www.gromacs.org/@api/deki/**files/74/=
>> **ConvertGromos2Gromacs.tgz<http://www.gromacs.org/@api/deki/files/74/=ConvertGromos2Gromacs.tgz>
>> >in
>> the user contributions, I do not see any other relevant scripts.
> That's probably what you need.  Is there some reason it does not work?
>  Can someone give me relevant pointers for undertaking this task? What
>> quantities should I calculate, etc (Justin recently computed single point
>> energies for creating a charmm36 port to gromacs...can you help me here?)
> We compared potential energies (bonded and nonbonded terms individually)
> between the CHARMM36 force field in the latest version of the CHARMM
> software, then our CHARMM36 port within Gromacs.  If the energies agreed,
> we were satisfied that the force field was implemented properly.  The same
> would apply here - if you want to validate between the two software
> packages, carry out equivalent calculations in both programs.
> -Justin
> --
> ==============================**====================
> Justin A. Lemkul, Ph.D.
> 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 <jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> ==============================**====================
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Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore

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