[gmx-users] confusion on NPT MD simulation

Justin Lemkul jalemkul at vt.edu
Thu Jun 18 13:34:24 CEST 2015 


On 6/18/15 6:28 AM, Ming Tang wrote:
> Dear Tsjerk and Justin,
>
> Thanks for your help. I have tried to use 1000 and 10000 to restrained the whole protein during NPT equilibration, but found the protein shape changed as well. Is position restraint compatible with pressure coupling?
>

Restraints are compatible with pressure coupling.  Too high of a restraint can 
generate spurious forces, as Tsjerk mentioned below.  Note that restraints are 
just biasing potentials; they can allow for small changes in the structure.  You 
shouldn't necessarily hike the force constant to some high value to try to 
absolutely fix the atoms.

-Justin

> Thanks very much.
>
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar
> Sent: Wednesday, 17 June 2015 1:53 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] confusion on NPT MD simulation
>
> Hi Ming Tang,
>
> You don't need a huge force constant to keep it fixed. Too high forces may give instabilities. And a more gentle one (100-1000) does the trick as well.
>
> Cheers,
>
> Tsjerk
> On Jun 17, 2015 4:17 AM, "Ming Tang" <m21.tang at qut.edu.au> wrote:
>
>> Dear Justin,
>>
>> Thank you so much.  There are another 2 papers in which the authors
>> said they equilibrated their  collagen like this. This really made me
>> confused for quite a  long time, and I come to you for help finally.
>> Critical analysis is important.
>>
>> In the "steps to perform a simulation" page, step 8  indicates that
>> NPT equilibration is for fixing the density. I have been confused
>> about how should I equilibrate my collagen before SMD simulation. I
>> want to keep the shape (do not change its length) of my collagen
>> during equilibration, so that the force-deformation curve will not be
>> changed because of the equilibration process. After knowing that
>> freezing and pressure coupling is incompatible, I tried to use NVT
>> with heavy atoms restrained by using -DPOSRES, and further the
>> simulation to SMD (actually umbrella and direction-periodic are used)
>> directly in NVT. The simulation run smoothly and I got my
>> force-deformation curve, but I am still concerned whether my
>> equilibration is good enough for SMD simulation, and whether the results are credible.
>> If I choose to further equilibrate my collagen in NPT after in NVT, is
>> it feasible to restrain parts (backbone, terminal atoms) of my
>> collagen by adding a huge force constant (say 1*10e6  kJ/mol/nm^2)
>> through -fc in genrestr command, so that its shape will be reserved
>> during the equilibration?
>>
>> Could you please kindly give me some guidance on which is the best
>> equilibration process I show follow to get a good starting point for
>> SMD
>> (umbrella+direction-periodic) simulation?
>>
>> Thank you so much.
>>
>> -----Original Message-----
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin
>> Lemkul
>> Sent: Tuesday, 16 June 2015 9:37 PM
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] confusion on NPT MD simulation
>>
>>
>>
>> On 6/16/15 5:27 AM, Ming Tang wrote:
>>> Dear Justin,
>>>
>>> I read a paper, in which the author equilibrated the collagen like this:
>>> Firstly, a 100 ps NVT MD simulation at a temperature 310 K was
>>> performed, in which velocity rescaling algorithm with 1ps coupling
>>> constant was used. Rigid bonds were used to constraint covalent bond
>>> length, allowing a time step of 2fs. Secondly, a 200ps NPT ensemble
>>> with 1bar pressure was used to equilibrate the system while keeping
>>> the temperature at 310 K, where Berendsen barostat with 1ps coupling
>>> constant was adopted. In this step, the whole protein was held fixed.
>>> Lastly, we further equilibrated the system in a NPT ensemble for
>>> 400ps, with a more accurate pressure coupling algorithm based on
>>> Parrinello-Rahman barostat (Parrinello and Rahman 1981). Only the
>>> first
>> and the last C − α atoms of each chain were constrained.
>>>
>>> I wonder whether they used genrestr to restrain atoms, like
>>> utilising -fc to add a quite large force in all directions to them,
>>> and considered those atoms are kept fixed during NPT equilibration?
>>>
>>
>> People are often lazy (or inconsistent) with language.  Holding
>> something "fixed" might mean "huge restraint" or it might actually
>> mean frozen (freezegrps in the .mdp).  There are functional
>> differences between these two.  Atoms are also not "constrained"
>> (that's a restraint!) in GROMACS, so there may be some loose language here...
>>
>> If you have questions about methods for published work relevant to
>> what you're doing, that's what corresponding authors are for!
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> 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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