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

Justin Lemkul jalemkul at vt.edu
Mon Aug 8 12:05:10 CEST 2016 


On 8/7/16 1:21 PM, Dan Gil wrote:
> In Gromacs/4.6, I used init to define the distance from the solvent COM
> that the solute should be pulled to. Has it changed for Gromacs/5.1?
>

Nothing has changed except (1) syntax and (2) the ability to now apply multiple 
restraints simultaneously.  Everything with respect to setting references 
distances, etc. is functionally the same.

> What should I do if I want to pull the solute to [0, 1, 2, 3] nm away from
> the solvent COM?
>

You can do that with "pull-coord1-init = X" and "pull-start = no" but this is 
setting the reference distance to X, so if the initial coordinates are far from 
that value, you're imparting a large force to start, which may not be stable. 
It may work, but those initial steps are going to be dicey.

-Justin

> Here is the section I think you are talking about also:
> Pull group 1 'a_Cooh' has 1 atoms
> Pull group 2 'SOL' has 5715 atoms
> Number of degrees of freedom in T-Coupling group System is 44530.00
> Pull group  natoms  pbc atom  distance at start  reference at t=0
>        1         1         0
>        2      5715     18540       3.011 nm          3.011 nm
>
> On Sun, Aug 7, 2016 at 1:15 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 8/7/16 1:13 PM, Dan Gil wrote:
>>
>>> 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.
>>>
>>>
>>>
>> pull-coord1-start        = yes
>>
>> grompp tells you what the reference distance is at the start; check to
>> make sure this is what you want it to be.  pull-coord1-init = 0 means
>> "don't add anything extra to what is already there."
>>
>>
>> -Justin
>>
>>
>>> 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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>>>>>>>
>>>>>>
>>>>>> --
>>>>>> 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
>>>>
>>>> ==================================================
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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

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

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