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

[Dan Gil]

Hi,

I've made the change you suggested. The output file pullx.xvg has changed
from something like:

@ s0 legend "1"
@ s1 legend "1 dZ"
0.0000 3.01072 3.01072
0.2000 2.98101 2.98101
0.4000 2.94186 2.94186
0.6000 2.95316 2.95316

to this:

@ s0 legend "1"
@ s1 legend "1 dZ"
0.0000 3.01072 -3.01072
0.2000 2.98101 -2.98101
0.4000 2.94186 -2.94186
0.6000 2.95316 -2.95316

The second column should the COM of the solvent, the third column should be
the position of a_Cooh. I am still wondering what is going on, since init =
0.



On Sun, Aug 7, 2016 at 11:37 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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>>>
>>>
>>> --
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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
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