[gmx-users] Change to umbrella sampling pull code

[Nash, Anthony]

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
-------------------------------------------------------


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
>>>>
>>>> --
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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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