[gmx-users] confusion on NPT MD simulation

[V.V.Chaban]

If your protein structure is retained, your procedure is all right.



On Mon, Jun 15, 2015 at 5:04 AM, Ming Tang <m21.tang at qut.edu.au> wrote:
> Dear Justin,
>
> I got a problem making me confused for weeks.
> I found 2 journals, in which the author kept parts of their protein to equilibrate their system in NPT. Is there any other methods to keep atoms fixed during NPT equilibrium besides freezing them?
> As you mentioned,  freezing and pressure coupling are incompatible. My first understanding was that I cannot fix atoms during NPT. Therefore, I have been steering my collagen in NVT recently.  After minimization, I equilibrated my collagen in NVT with the heavy atoms restrained (define = -DPOSRES) for 20ns, and then stretched it using pull code. Do you think this simple process can give a good starting point for SMD?
>
> 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 Justin Lemkul
> Sent: Monday, 1 June 2015 9:46 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] confusion on NPT MD simulation
>
>
>
> On 6/1/15 4:40 AM, Ming Tang wrote:
>> Dear gromacs experts,
>>
>> I tried to equilibrate a triple helix using NPT, and the .mdp file is like this:
>>
>> DEFINE           =  -DPOSRES
>> integrator       =  md
>> dt               =  0.0009
>> nsteps           =  1000000
>> nstxout          =  0
>> nstvout          =  0
>> nstlog           =  10000
>> nstxtcout        =  10000
>> xtc-precision    =  10
>> cutoff-scheme    =  verlet
>> coulombtype      =  reaction-field-zero
>> coulomb-modifier =  potential-shift-verlet rcoulomb-switch  =  0.8
>> rcoulomb         =  1.4
>> epsilon_r        =  15
>> vdw-modifier     =  force-switch
>> rvdw-switch      =  0.8
>> rvdw             =  1.4
>> tcoupl           =  v-rescale
>> tc-grps          =  Protein non-protein
>> tau-t            =  1.0 1.0
>> ref-t            =  310 310
>> Pcoupl           =  parrinello-Rahman
>> Pcoupltype       =  isotropic
>> tau-p            =  5
>> compressibility  =  3e-4
>> ref-p            =  1.0
>> refcoord_scaling =  all
>> pbc              =  xyz
>> freezegrps       =  C
>> freezedim        =  Y Y Y
>>
>> C is a group containing atoms of both the first and the last residues in all the three chains.
>> But after 18ns' simulation, I found the one end of the triple helix moved. Could you help to tell me whether this is normal or there is something wrong with my simulation?
>> Then, I tried to use berendsen for both tcoupl and pcoupl. It turned out that both ends were fixed.  I need to keep the original geometry shape of the triple helix, but berendsen algorithm is believed to be inaccurate.
>>
>
> Freezing and pressure coupling are incompatible; see notes in the manual.
>
> -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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