[gmx-users] parameters problem
Nidhi Katyal
nidhikatyal1989 at gmail.com
Mon Mar 10 07:45:10 CET 2014
Thank you Mark and Justin.
Now, I have carried out simulations using PME electrostatics and using all
other parameters (except gromos 96 43a1 ff used) as suggested in
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
The protein is not loosing its structure now. But the problem is if I carry
out simulations in the presence of experimentally known stabiliser
generated using ProDrg (keeping all the parameters same while simulating
both in the presence and absence of stabiliser), the partial loss of
secondary structure is observed in the presence of stabilizer relative to
the case in its absence at 350K thereby implying simulations going against
experimental observations (although slight stabilization was observed at
300K). Simulations were repeated twice with two different force fields.
However if I use above em,pr,full parameters with cut-off electrostatics,
although secondary structure is lost in the initial stages but I could
clearly see the stabilization behaviour of additive in terms of secondary
structure retainment till longer time. Is this observation a matter of
chance- reliable or not? What could be the possible reason for not
observing such stabilization with better parameters?
Looking forward to your reply.Thanks in advance.
Nidhi
On Mon, Feb 17, 2014 at 7:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 2/17/14, 4:16 AM, Nidhi Katyal wrote:
>
>> Dear all
>>
>> I am trying to simulate a protein in 3 steps: energy minimization (using
>> em.mdp), position restraints (using pr.mdp) and final production run by
>> NPT
>> ensemble (using full.mdp) at 300K
>>
>> At this temperature, it is known by previous literature survey that
>> protein
>> keeps its secondary structure almost intact. But according to my
>> simulations (done thrice), protein starts loosing its secondary structure
>> around 6-8ns only. I have used the following parameters:
>>
>> *em.mdp*
>>
>> ;
>> ; User spoel (236)
>>
>> ; Wed Nov 3 17:12:44 1993
>> ; Input file
>> ;
>> cpp = /usr/bin/cpp
>> define = -DFLEX_SPC
>> constraints = none
>> integrator = steep
>> nsteps = 250000
>> ;
>> ; Energy minimizing stuff
>> ;
>> emtol = 2000
>> emstep = 0.001
>>
>> nstcomm = 1
>> ns_type = grid
>> rlist = 1
>> rcoulomb = 1.0
>> rvdw = 1.0
>> Tcoupl = no
>> Pcoupl = no
>> gen_vel = no
>>
>>
>> *pr.mdp*
>>
>> ;
>> ; User spoel (236)
>>
>> ; Wed Nov 3 17:12:44 1993
>> ; Input file
>> ;
>> title = Yo
>> cpp = /usr/bin/cpp
>> define = -DPOSRES
>> constraints = all-bonds
>> integrator = md
>> dt = 0.002 ; ps !
>> nsteps = 50000 ; total 100 ps.
>> nstcomm = 1
>> nstxout = 5000
>> nstvout = 5000
>> nstfout = 0
>> nstlog = 10
>> nstenergy = 10
>> nstlist = 10
>> ns_type = grid
>> rlist = 1.0
>> rcoulomb = 1.0
>> rvdw = 1.0
>> ; Berendsen temperature coupling is on in two groups
>> Tcoupl = berendsen
>> tc-grps = Protein Non-protein
>> tau_t = 0.1 0.1
>> ref_t = 300 300
>> ; Energy monitoring
>> energygrps = Protein Non-protein
>> ; Pressure coupling is not on
>> Pcoupl = no
>> tau_p = 0.5
>> compressibility = 4.5e-5
>> ref_p = 1.0
>> ; Generate velocites is on at 300 K.
>> gen_vel = yes
>> gen_temp = 300.0
>> gen_seed = 173529
>>
>>
>> *full.mdp*
>>
>> ;
>> ; User spoel (236)
>>
>> ; Wed Nov 3 17:12:44 1993
>> ; Input file
>> ;
>> title = Yo
>> cpp = /usr/bin/cpp
>> constraints = all-bonds
>> integrator = md
>> dt = 0.002 ; ps !
>> nsteps = 25000000 ; total 50000 ps.
>> nstcomm = 1
>> nstxout = 5000
>> nstvout = 5000
>> nstfout = 0
>> nstlog = 5000
>> nstenergy = 5000
>> nstlist = 10
>> ns_type = grid
>> rlist = 1.0
>> rcoulomb = 1.0
>> rvdw = 1.0
>> ; Berendsen temperature coupling is on in two groups
>> Tcoupl = berendsen
>> tc-grps = Protein Non-protein
>> tau_t = 0.1 0.1
>> ref_t = 300 300
>> ; Energy monitoring
>> energygrps = Protein Non-protein
>> ; Isotropic pressure coupling is now on
>> Pcoupl = berendsen
>> Pcoupltype = isotropic
>> tau_p = 0.5
>> compressibility = 4.5e-5
>> ref_p = 1.0
>> ; Generate velocites is off at 300 K.
>> gen_vel = no
>> gen_temp = 300.0
>> gen_seed = 173529
>>
>> I don't think it is the problem of thermostat because even after using
>> V-rescale for temperature coupling and Parinello Rahman for pressure
>> coupling, my protein loses its secondary structure in the initial time of
>> simulation.
>>
>> Also, I have carried out various checks (like potential energy convergence
>> after em, temperature check after pr, and pressure and density check after
>> full), all of which seems to converge well.
>>
>> Please help me figure out the problem.
>>
>>
> The more relevant information is which force field you are using. It is
> also possible that the introduction of pressure coupling without restraints
> can cause screwy behavior, so a restrained NPT equilibration is probably
> worthwhile, as well.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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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