[gmx-users] Change to umbrella sampling pull code

Wed Aug 12 23:01:20 CEST 2015

On 8/12/15 4:51 PM, Nash, Anthony wrote:
> Thanks for clearing that up Justin, I’ve adjusted accordingly. All but one
> error remains:
>
>
> Pull group 1 'ZINC' has 1 atoms
> Pull group 2 'CARBONYL' has 1 atoms
>
> -------------------------------------------------------
> Program grompp, VERSION 5.0.5
> Source code file:
> /home/columbus/chem_software/GROMACS/2015/gromacs-5.0.5/src/gromacs/gmxprep
> rocess/readpull.c, line: 377
>
>
> Fatal error:
> Identical pull group indices in pull-coord1-groups
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
>

You need:

pull-coord1-groups = 1 2

otherwise the reaction coordinate is undefined, or otherwise defaults to the 
entire system, I can't remember which.

-Justin

> The entries in my index.ndx are:
>
> [ ZINC ]
> 5809
> [ CARBONYL ]
> 6481
>
>
> For the respective .mdp entries (pull code):
>
> ; Pull code
> pull            = umbrella
> pull_geometry   = distance
> pull_dim        = Y Y Y
> pull_start      = yes
> pull_ngroups    = 2
> pull_group1_name = ZINC
> pull_group2_name = CARBONYL
> pull_coord1_init = 0
> pull_coord1_rate = 0
> pull_coord1_k = 1000
> pull_nstxout    = 1000      ; every 2 ps
> pull_nstfout    = 1000      ; every 2 ps
>
>
>
>
> On 12/08/2015 21:26, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 8/12/15 3:20 PM, Nash, Anthony wrote:
>>> Hi Mark,
>>>
>>> Thanks for the reply.
>>>
>>> Comparing the documentation between manual-4.5.6 (what I had previously
>>> been using) and manual-5.0.4:
>>>
>>> 4.5.6 has reference to pull_group0 as reference group, and in 5.0.4
>>> there
>>> is no explicit mention (that I can see) to a reference group but there
>>> is
>>> one for the pull group (pull-group1-name).
>>>
>>
>> Right, because multiple reaction coordinates can now be simultaneously be
>> restrained.  There is no requirement for a single reference group.  Any
>> combination of groups can be used.  Offhand, your settings are right
>> except
>> pull-ngroups is 2, as there are two groups.
>>
>> -Justin
>>
>>> Thanks
>>> Anthony
>>>
>>> Dr Anthony Nash
>>> Department of Chemistry
>>> University College London
>>>
>>>
>>>
>>>
>>>
>>> On 12/08/2015 19:35, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
>>>
>>>> Hi,
>>>> On Wed, Aug 12, 2015 at 6:20 PM Nash, Anthony <a.nash at ucl.ac.uk> wrote:
>>>>
>>>>> Dear all,
>>>>>
>>>>> This is the first time I¹ve ran pull code (for umbrella sampling)
>>>>> since
>>>>> the change from Gromacs 4 to gromancs 5. I¹ve noticed some difference
>>>>> in
>>>>> the .mdp key-value parameters. Could I have a sanity check on the
>>>>> values
>>>>> below.
>>>>
>>>>
>>>> I have no real idea, but you could start by comparing the respective
>>>> documentation. If something's not clear, that's something to fix ;-)
>>>>
>>>> Also, given that I want a harmonic potential between the two
>>>>> groups, does it matter which index group is assigned to the respective
>>>>> Œpull-groupN-name¹ key?
>>>>>
>>>>
>>>> I doubt it, but if you want a definitive answer, make yourself a toy
>>>> test
>>>> case and see.
>>>>
>>>> Mark
>>>>
>>>>
>>>>> Note: my reaction coordinate was defined initially following the
>>>>> trajectory between two minima during a meta-dynamics MD simulation.
>>>>> That
>>>>> too was distance based.
>>>>>
>>>>>
>>>>> ;Pull code
>>>>> pull            = umbrella
>>>>> pull-geometry   = distance
>>>>> pull-dim        = Y Y Y
>>>>> pull-start      = yes
>>>>> pull-ngroups    = 1
>>>>> pull-group1-name = ZINC
>>>>> pull-group2-name = CARBONYL
>>>>> pull-coord1-init = 0
>>>>> pull-coord1-rate = 0
>>>>> pull-coord1-k = 1000
>>>>> pull-nstxout    = 1000      ; every 2 ps
>>>>> pull-nstfout    = 1000      ; every 2 ps
>>>>>
>>>>>
>>>>> Many thanks
>>>>> Anthony
>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
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>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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