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

[Gianluca Interlandi]

On Sat, 9 Nov 2013, Gianluca Interlandi wrote:

Just to chime in. Here is a that paper might be helpful in understanding 
the role of cuoffs in the CHARMM force field:

AU STEINBACH, PJ
    BROOKS, BR
AF STEINBACH, PJ
    BROOKS, BR
TI NEW SPHERICAL-CUTOFF METHODS FOR LONG-RANGE FORCES IN MACROMOLECULAR
    SIMULATION
SO JOURNAL OF COMPUTATIONAL CHEMISTRY
SN 0192-8651
PD JUL
PY 1994
VL 15
IS 7
BP 667
EP 683
DI 10.1002/jcc.540150702
UT WOS:A1994NU17400001

Gianluca

> On Sat, 9 Nov 2013, Justin Lemkul wrote:
>
>> 
>> 
>> On 11/9/13 4:16 PM, rajat desikan wrote:
>>> Hi Justin,
>>> I take it that both the sets of parameters should produce identical
>>> macroscopic quantities.
>>> For the GPU, is this a decent .mdp?
>>> 
>>> cutoff-scheme    = Verlet
>>> vdwtype             = switch
>>> rlist                    = 1.2
>>> ;rlistlong             = 1.4                     NOT USED IN GPU...IS THIS
>>> OK?
>>> rvdw                   = 1.2
>>> ;rvdw-switch        = 1.0                    NOT USED IN GPU...IS THIS OK?
>>> coulombtype       = pme
>>> DispCorr             = EnerPres
>>> rcoulomb            = 1.2
>>> 
>> 
>> I have no basis for saying whether or not it will produce correct results. 
>> I have never tested this force field on GPU with the Verlet scheme.  My 
>> biggest concern is with the treatment of van der Waals interactions, and I 
>> have not used the Verlet scheme enough to understand what it is doing and 
>> how it will treat the interactions that should be switched.  If someone 
>> else can comment, that would be useful to me, as well!
>> 
>> Test carefully and please report back.  A comparison between CPU and GPU 
>> would be very valuable.
>> 
>> -Justin
>> 
>>> 
>>> On Fri, Nov 8, 2013 at 7:19 PM, Justin Lemkul [via GROMACS] <
>>> ml-node+s5086n5012351h26 at n6.nabble.com> wrote:
>>> 
>>>> 
>>>> 
>>>> On 11/7/13 11:32 PM, Rajat Desikan wrote:
>>>> 
>>>>> Dear All,
>>>>> The setting that I mentioned above are from Klauda et al., for a POPE
>>>>> membrane system. They can be found in charmm_npt.mdp in lipidbook (link
>>>>> below)
>>>>> http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html
>>>>> 
>>>>> Is there any reason not to use their .mdp parameters for a
>>>> membrane-protein
>>>>> system? Justin's recommendation is highly valued since I am using his
>>>>> forcefield. Justin, your comments please
>>>>> 
>>>> 
>>>> Careful now, it's not "my forcefield."  I derived only a very small part
>>>> of it :)
>>>> 
>>>>> To summarize:
>>>>> Klauda et al., suggest
>>>>> rlist                      = 1.0
>>>>> rlistlong                = 1.4
>>>>> rvdw_switch          = 0.8
>>>>> vdwtype                = Switch
>>>>> coulombtype          = pme
>>>>> DispCorr                = EnerPres     ;only usefull with reaction-field
>>>>> and pme or pppm
>>>>> rcoulomb               = 1.0
>>>>> rcoulomb_switch    = 0.0
>>>>> rvdw                     = 1.2
>>>>> 
>>>>> Justin's recommendation (per mail above)
>>>>> vdwtype = switch
>>>>> rlist = 1.2
>>>>> rlistlong = 1.4
>>>>> rvdw = 1.2
>>>>> rvdw-switch = 1.0
>>>>> rcoulomb = 1.2
>>>>> 
>>>> 
>>>> The differences between these two sets of run parameters are very small,
>>>> dealing
>>>> mostly with Coulomb and neighbor searching cutoffs.  I would suspect that
>>>> any
>>>> difference between simulations run with these two settings would be
>>>> similarly
>>>> small or nonexistent, given that rcoulomb is a bit flexible when using
>>>> PME.  The
>>>> value of rlist is rarely mentioned in papers, so it is good that the
>>>> authors
>>>> have provided the actual input file.  Previous interpretation of CHARMM
>>>> usage
>>>> generally advised setting rcoulomb = 1.2 to remain consistent with the
>>>> original
>>>> switching/shifting functions.  That setting becomes a bit less stringent
>>>> when
>>>> using PME.
>>>> 
>>>> -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
>>>> 
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>>> 
>>> 
>> 
>> -- 
>> ==================================================
>> 
>> 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 | (410) 706-7441
>> 
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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.
> -----------------------------------------------------

-----------------------------------------------------
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.
-----------------------------------------------------