[gmx-users] Upgrading to Gromacs/5.1 - Problems with Umbrella Sampling
Dan Gil
dgilgmx at gmail.com
Mon Aug 8 16:24:35 CEST 2016
I see. Now I understand what "pull-start" option means. Changing that
option made it work! Thank you Justin.
On Mon, Aug 8, 2016 at 6:04 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>>>>>
>>>>> ==================================================
>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
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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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> Gromacs Users mailing list
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