[gmx-users] PR

[Zhe Wu]

Thank you for the discussion. I am basically having a similar problem:
position restraining (PR) 2 plates in NPT and the system blow up
(posted here: http://lists.gromacs.org/pipermail/gmx-users/2010-November/055975.html).
I will try to use smaller time step to see whether the situation
becomes better. A quick question, can we really do meaningful NPT
simulation with PR, in which the position need to be almost like
fixed? I know we cannot do freeze. PR supposed to be OK, right?

Thanks,
Zhe

On Sun, Nov 21, 2010 at 9:51 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 21/11/2010 9:09 PM, pawan raghav wrote:
>>
>> Thank mark for comments, but I have check the structure after energy
>> minimization through ramachandran plot and found 82% residues were lies in
>> core region. After performed position restrained dynamics it reduced to 52%
>> in core region also 1 bad contact was found. I have taken SPC water model
>> then add 2 NA+ ions in the solvent, done energy minimization at emtol value
>> of 2000 kJ/mol and steps for 250. Below is the pr.mdp file for position
>> restraiuned dynamics, please let me know if any serious flaws. So help me by
>> giving me the reference.
>>
>> title = Position restrained of Bcl-2.
>>
>> integrator = md
>>
>> define = -DPOSRES
>>
>> dt = 0.002
>>
>
> A smaller timestep during equilibration will better help the integration
> cope with anything that is not very happy.
>
>> nsteps = 100000
>>
>> nstcomm = 1
>>
>> nstxout = 250
>>
>> nstvout = 1000
>>
>> nstfout = 0
>>
>> nstlog = 10
>>
>> nstenergy = 10
>>
>> nstlist = 5
>>
>> xtc_grps = protein sol
>>
>> energygrps = protein sol
>>
>> ns_type = grid
>>
>> rlist = 1.0
>>
>> coulombtype = PME
>>
>> rcoulomb = 1.0
>>
>> vdwtype = cut-off
>>
>> rvdw = 1.4
>>
>> fourierspacing = 0.135
>>
>> fourier_nx = 0
>>
>> fourier_ny = 0
>>
>> fourier_nz = 0
>>
>> pme_order = 4
>>
>> ewald_rtol = 1e-5
>>
>> optimize_fft = yes
>>
>> Dispcorr = no
>>
>> Tcoupl = v-rescale
>>
>> tc-grps = protein sol NA+
>>
>
> Those groups are bad. See
> http://www.gromacs.org/Documentation/Terminology/Thermostats
>
> Mark
>
>> tau_t = 0.1 0.1 0.1
>>
>> ref_t = 300 300 300
>>
>> Pcoupl = parrinello-rahman
>>
>> Pcoupltype = isotropic
>>
>> tau_p = 0.5
>>
>> compressibility = 4.5e-5
>>
>> ref_p = 1.0
>>
>> gen_vel = yes
>>
>> gen_temp = 300.0
>>
>> gen_seed = 173529
>>
>> constraints = all-bonds
>>
>>
>>
>> --
>> Pawan
>
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