[gmx-users] Re: CHARMM .mdp settings for GPU

[Gianluca Interlandi]

Hi Mark!

I think that this is the paper that you are referring to:

dx.doi.org/10.1021/ct900549r

Also for your reference, these are the settings that Justin recommended 
using with CHARMM in gromacs:

vdwtype = switch
rlist = 1.2
rlistlong = 1.4
rvdw = 1.2
rvdw-switch = 1.0
rcoulomb = 1.2

As you mention the switch function in gromacs is different than in CHARMM 
but it appears that the difference is very small.

Gianluca

On Thu, 7 Nov 2013, Mark Abraham wrote:

> Reasonable, but CPU-only is not 100% conforming either; IIRC the CHARMM
> switch differs from the GROMACS switch (Justin linked a paper here with the
> CHARMM switch description a month or so back, but I don't have that link to
> hand).
>
> Mark
>
>
> On Thu, Nov 7, 2013 at 8:45 PM, rajat desikan <rajatdesikan at gmail.com>wrote:
>
>> Thank you, Mark. I think that running it on CPUs is a safer choice at
>> present.
>>
>>
>> On Thu, Nov 7, 2013 at 9:41 PM, Mark Abraham <mark.j.abraham at gmail.com
>>> wrote:
>>
>>> Hi,
>>>
>>> It's not easy to be explicit. CHARMM wasn't parameterized with PME, so
>> the
>>> original paper's coulomb settings can be taken with a grain of salt for
>> use
>>> with PME - others' success in practice should be a guideline here. The
>> good
>>> news is that the default GROMACS PME settings are pretty good for at
>> least
>>> some problems (http://pubs.acs.org/doi/abs/10.1021/ct4005068), and the
>> GPU
>>> auto-tuning of parameters in 4.6 is designed to preserve the right sorts
>> of
>>> things.
>>>
>>> LJ is harder because it would make good sense to preserve the way CHARMM
>>> did it, but IIRC you can't use something equivalent to the CHARMM LJ
>> shift
>>> with the Verlet kernels, either natively or with a table. We hope to fix
>>> that in 5.0, but code is not written yet. I would probably use vdwtype =
>>> cut-off, vdw-modifier = potential-shift-verlet and
>> rcoulomb=rlist=rvdw=1.2,
>>> but I don't run CHARMM simulations for a living ;-)
>>>
>>> Mark
>>>
>>>
>>> On Thu, Nov 7, 2013 at 1:42 PM, Rajat Desikan <rajatdesikan at gmail.com
>>>> wrote:
>>>
>>>> Dear All,
>>>>
>>>> Any suggestions?
>>>>
>>>> Thank you.
>>>>
>>>> --
>>>> View this message in context:
>>>>
>>>
>> http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012316.html
>>>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>>>> --
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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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-----------------------------------------------------
Gianluca Interlandi, PhD gianluca at u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------