[gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling

[Justin Lemkul]

On 8/7/16 11:35 AM, Dan Gil wrote:
> Hi,
>
> The pullx.xvg file is returning the coordinates of the solvent, and not the
> solute (a_Cooh) as I want.
> The solute is being pulled in a coordinate other than Z, although I specify:
>  pull-coord1-dim =N N Y
> What is going on here?
>

Swap
pull-coord1-groups     = 1 2
for
pull-coord1-groups     = 2 1

to do what you had been doing in the previous version.  You've inverted the pull 
vector relative to the 4.6 settings.

-Justin

> On Sun, Aug 7, 2016 at 7:20 AM, Billy Williams-Noonan <
> billy.williams-noonan at monash.edu> wrote:
>
>> Hi All,
>>
>> I'm having a similar problem and wouldn't mind some advice either.  I am
>> getting LINCS warnings on one cluster that I run my sampling on, but the
>> pull-code works fine on other clusters we have access to, which is making
>> me doubt the entire process.
>>
>> Best regards,
>>
>> Billy
>>
>> On 7 August 2016 at 03:34, Dan Gil <dgilgmx at gmail.com> wrote:
>>
>>> Hi,
>>>
>>> I am changing from Gromacs/4.6 to Gromacs/5.1, and I have a piece of .mdp
>>> file that I am confused with.
>>>
>>> I am pulling an atom of solute, indexed a_Cooh, towards the COM of
>> solvent.
>>> This is a slab geometry, with the plane normal to the z-axis direction.
>> My
>>> output (pullx.xvg) should contain the deltaZ value between the solute Z
>>> coordinate and solvent COM z coordinate. With my current Gromacs/5.1
>>> attempt, I don't think I am getting the correct results.
>>>
>>> On Gromacs/4.6:
>>> pull =umbrella
>>> pull_geometry =distance
>>> pull_dim =N N Y
>>> pull_init1 =0
>>> pull_k1 =100
>>> pull_nstxout =100
>>> pull_group0 =SOL
>>> pull_group1 =a_Cooh
>>>
>>> My attempt with Gromacs/5.1:
>>> pull =yes
>>> pull-ngroups        = 2
>>> pull-ncoords        = 1
>>> pull-group1-name = a_Cooh
>>> pull-group2-name = SOL
>>> pull-coord1-type  = umbrella
>>> pull-coord1-geometry =distance
>>> pull-coord1-groups     = 1 2
>>> pull-coord1-dim =N N Y
>>> pull-coord1-start        = yes
>>> pull-coord1-init          =0
>>> pull-coord1-k        =1000
>>> pull-print-components = yes
>>> pull_nstxout =100
>>>
>>> Best Regards,
>>>
>>> Dan
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>>
>>
>>
>> --
>> Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
>>
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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

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