[gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling
Dan Gil
dgilgmx at gmail.com
Sun Aug 7 19:21:46 CEST 2016
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?
What should I do if I want to pull the solute to [0, 1, 2, 3] nm away from
the solvent COM?
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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