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

[Justin Lemkul]

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
>>
>> [hidden email] <http://user/SendEmail.jtp?type=node&node=5012351&i=0> |
>> (410) 706-7441
>>
>> ==================================================
>> --
>> gmx-users mailing list    [hidden email]<http://user/SendEmail.jtp?type=node&node=5012351&i=1>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to [hidden email]<http://user/SendEmail.jtp?type=node&node=5012351&i=2>.
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>> ------------------------------
>>   If you reply to this email, your message will be added to the discussion
>> below:
>>
>> http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012351.html
>>   To unsubscribe from CHARMM .mdp settings for GPU, click here<http://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=5012267&code=cmFqYXRkZXNpa2FuQGdtYWlsLmNvbXw1MDEyMjY3fDM0NzUwNzcwNA==>
>> .
>> NAML<http://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>>
>
>
>

-- 
==================================================

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

==================================================