[gmx-users] Pressure coupling and cut-off
Yanmei Song
ysong30 at asu.edu
Fri May 15 18:53:38 CEST 2009
Dear Justin:
Thank you for your suggestions. using shift for vdwtype helps a lot.
Can I ask you another question? The density of my system is about 8% larger
than the experimental value. Do you have any suggestions on how to reduce
the density of the system. Or once the force field and all the parameters
are fixed, the density is independent of the MD procedure? I am using NPT
ensemble with the mdp I mentioned before with added vdwtype = shift.
On Thu, May 14, 2009 at 4:35 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Yanmei Song wrote:
>
>> Dear Justin:
>>
>> Thanks for your response. Here is the complete my .mdp file:
>>
>> title = pdm
>> cpp = /lib/cpp
>> constraints = all_bonds
>> integrator = md
>> dt = 0.004 ; ps !
>> nsteps = 2500000 ; total 10ns.
>> nstcomm = 1
>> nstxout = 50000
>> nstvout = 50000
>> nstfout = 0
>> nstlog = 5000
>> nstenergy = 5000
>> nstxtcout = 25000
>> nstlist = 10
>> ns_type = grid
>> pbc = xyz
>> coulombtype = PME
>> rlist = 1.4
>> rcoulomb = 1.4
>> rvdw = 1.4
>> fourierspacing = 0.20
>> pme_order = 4
>> ewald_rtol = 1e-5
>> ; Berendsen temperature coupling is on in one groups
>> Tcoupl = berendsen
>> tc_grps = PDM
>> tau_t = 0.1
>> ref_t = 300
>> ; Energy monitoring
>> energygrps = PDM
>> ; Isotropic pressure coupling is now on
>> Pcoupl = berendsen
>> pcoupltype = isotropic
>> ;pc-grps = PDM
>> tau_p = 1.0
>> ref_p = 1.0
>> compressibility = 4.5e-5
>>
>> ; Generate velocites is off at 300 K.
>> gen_vel = yes
>> gen_temp = 300.0
>> gen_seed = 100000
>>
>>
>>
> The problem you're seeing could be an artifact of the shorter cutoff. Have
> you tried using DispCorr = EnerPres? Or what about using a Shift function
> for vdwtype? You might see better energy conservation in that case compared
> to a plain cutoff.
>
> -Justin
>
>
>> On Thu, May 14, 2009 at 4:06 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>> Yanmei Song wrote:
>>
>> Dear All:
>>
>> I have question about the pressure coupling. I have done a 10ns
>> simulation with 19800 atoms for 120 large molecules using the
>> following pressure coupling.
>>
>> Tcoupl = berendsen
>> tc_grps = PDM
>> tau_t = 0.1
>> ref_t = 300
>>
>> Pcoupl = berendsen
>> pcoupltype = isotropic
>> ;pc-grps = PDM
>> tau_p = 1.0
>> ref_p = 1.0
>> compressibility = 4.5e-5
>>
>> Then I did g_energy for the last 3ns and got the results:
>>
>> Energy Average RMSD Fluct.
>> Drift Tot-Drift
>>
>> -------------------------------------------------------------------------------
>> Potential -98061 0 0
>> 0.61668 1850.04
>> Temperature 303.561 109.602 109.602
>> 0.000181791 0.545372
>> Pressure (bar) 4.4884 11110.8 11109.8
>> -0.169835 -509.506
>>
>> For such a long run the pressure drift is still too much and
>> seem hasn't approached 1bar. Does it mean the system hasn't
>> reach equilibrium yet. I did a similar system by using the same
>> method. it just take 2 or 3ns to reach the equilibrium. and the
>> pressure is around 1.01after the run. The only difference is the
>> cutoff changing from 1.2 to 1.4. Does the cufoff of 1.4 is too
>> large to make the system running slower. Or the pressure
>> coupling method is not working well. Anyone can give me any
>> suggestions?
>>
>>
>>
>> I think it will depend on the interplay of other parameters as well.
>> Posting a complete .mdp file may be more helpful.
>>
>> -Justin
>>
>> -- Yanmei Song
>> Ph.D. Candidate
>> Department of Chemical Engineering
>> Arizona State University
>>
>>
>>
>> ------------------------------------------------------------------------
>>
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>>
>> -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
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>>
>>
>>
>>
>> --
>> Yanmei Song
>> Ph.D. Candidate
>> Department of Chemical Engineering
>> Arizona State University
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
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