[gmx-users] Does Gmx 5.0 on GPUs support CMAP in Charmm?

[Justin Lemkul]

On 9/15/14 8:08 AM, Steven Neumann wrote:
> On Mon, Sep 15, 2014 at 7:46 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> On Mon, Sep 15, 2014 at 10:49 AM, Steven Neumann <s.neumann08 at gmail.com>
>> wrote:
>>
>>> Thanks! Was it different in previous GMX versions? It is stated that
>>> gromacs 4.6 does not support CMAP but nothing about 5.0 version that this
>>> was fixed.
>>>
>>
>> Really? Where?
>>
>
> http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GROMACS-OpenMM
>
>
>     - *Force Fields*: Supported FF are Amber, CHARMM. GROMOS and OPLS-AA are
>     not supported.
>        - CMAP dihedrals in CHARMM are not support, so use the *-nocmap*
>        option with pdb2gmx.
>

Within the context of OpenMM, that was true several years ago.  None of that is 
relevant, as OpenMM is no longer used by Gromacs in the native GPU acceleration.

-Justin

>
>
>>
>>
>>> How can I potentially check this it is correctly captured?
>>>
>>
>> Do two reruns with nstfout=1, one on only the CPU and the other with GPU,
>> and observe that the forces and energies are the same.
>>
>> Mark
>>
>>
>>>
>>>
>>> On Mon, Sep 15, 2014 at 3:17 PM, Mark Abraham <mark.j.abraham at gmail.com>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> That's very likely. GPU support in 5.0 is only for non-bonded
>>> interactions,
>>>> and CMAP is a bonded interaction. Of course, you could try it and see
>> ;-)
>>>>
>>>> Mark
>>>>
>>>> On Mon, Sep 15, 2014 at 4:56 AM, Steven Neumann <s.neumann08 at gmail.com
>>>
>>>> wrote:
>>>>
>>>>> Please, advise.
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>> posting!
>>>>>
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>> * For (un)subscribe requests visit
>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or
>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>> posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

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