On 10/24/13 9:00 AM, rajat desikan wrote:
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.
I doubt there have been any significant changes.
"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!
Reproducing published results is also a reasonable approach. Single-point
energies are the most straightforward and take but a few seconds, so they are
very convenient.
-Justin
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 <jalem...@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
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University of Maryland, Baltimore
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jalem...@outerbanks.umaryland.edu | (410) 706-7441
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