[gmx-users] Extending a run for different number of nodes
Justin A. Lemkul
jalemkul at vt.edu
Sun Sep 14 13:05:28 CEST 2008
DimitryASuplatov wrote:
> Hello,
> I have completed a 10ns run. Now I want to extend it to 20ns. The
> problem is that the initial tpr was compiled for 8 processors and now
> I have only 4 cores.
> What I tried to do is used tpbconv to make a 10ns extended tpr, then
> used an exactly the same mdp file to grompp it all together with -np 4
> to a new tpr file.
What do you mean "grompp it all together?" It sounds like you are trying to use
both tpbconv and grompp for some reason. The only way to change the number of
processors is to use grompp, not tpbconv, providing it your .trr and .edr files
with the -t and -e flags.
> The problem is that at the beginning of the trajectory the structure
> is undergoing a structural change with 0.12 nm from the initial
> structure. That means that the structure is actually relaxed and that
> is not something I want to see.
How do you know this is not the normal behavior?
-Justin
> I have used this in my mdp
> ;------------ VELOCITY INITIATION -----------------------
> gen-vel = no
> gen-temp = 300
>
> That means that no velocities were generated and I expect to see no
> relaxation but the continuation of my run.
>
> What am I doing wrong? How to extend a run without relaxation.
> Thank you. I appreciate any help.
> SDA
>
> My mdp file is the following.
> ;-------------PREPROCESSING OPTIONS------------
> title = PR "1KLC FREE"; my title
> cpp = cpp; my C prepocessor (whereIsIt)
> include = ; dir to include in my topology file
> define = ;
>
> ;-------------RUN CONTROL---------------------
> integrator = md;
>
> ;--------------OUTPUT CONTROL------------------
> ;TRR outpur
> nstxout = 10000
> nstvout = 10000
> nstfout = 0
>
> ;LOG and EDR output
> nstlog = 10000
> nstenergy = 10000
>
> ;XTC output
> nstxtcout = 1000
> xtc-precision = 1000
>
> ;-------------START TIME & TIMESTEP-----------
> tinit = ; [ps] starting time for your run (only makes
> sense for md, sd, bd integator)
> dt = 0.005 ; [ps] time step for integration (--"--)
> nsteps = 1600000 ; (0) maximum number of steps to integrate
> comm-mode = ; Linear(Remove center of mass
> translation)/Annular(Remove center of mass
> ;translation and rotation)/No(no restriction)
> nstcomm = 1
>
> ;-------------NEIGHBOR SEACHING---------------
>
> nstlist = 5; frequency o update
> neighbor list
> ns_type = grid; make a gid in
> the box and check only
> ;neighboring grid cell when constructing a new neighbor list
> rlist = 1.0; cut-off distance
> for the short-range neighbor list
>
> ;-------------ELECTROSTATICS------------------
> coulombtype = Reaction-field ; reaction field with
> coulomb cut-off rcoulomb
> ; where rcoulomb>rlist. The dielectric constant beyond the cut-off is epsilon_r
> rcoulomb = 1.5 ;distance for the
> coulomb cut-off
> epsilon_rf = 80;dielectric constant
> epsilon_r = 1;
>
> vdwtype = cut-off; twin-range
> cut-off`s with neighbor list cut-off rlist
> ;and VdW cut-off rvdw, where rvdw>rlist
> rvdw = 1.0 ; distance for for
> the LJ or Buckingam cut-off
>
> ;-------------ENERGY MINIMIZATION-------------
> emtol = 200 (kJ/mol*nm); minimisation is converged when
> the maximum force is smaller then this value
> emstep = 0.01; initial step size
>
> ;-------------TEMTERAURE CONTROL--------------
> tcoupl = berendsen
> tc-grps = System
> tau-t = 0.1
> ref-t = 300
>
> ;--------- PRESSURE CONTROL---------------------
> Pcoupl = no
> Pcoupltype = Isotropic
> tau-p = 1
> ref_p = 1
> compressibility = 4.5E-5
>
> ;------------ VELOCITY INITIATION -----------------------
> gen-vel = no
> gen-temp = 300
>
> ;------------- BONDS -----------------------
> constraints = all-bonds
> constraint-algorithm = Lincs
> unconstrained-start = yes
> Shake-SOR = no
> shake-tol = 0.0001
> lincs-order = 8
> lincs-warnangle = 30
> lincs-iter = 8
> morse = no
>
> sda at leiden:~/klc/MD/free> cat pr_free.extendfrom12to20ns.mdp
> ;-------------PREPROCESSING OPTIONS------------
> title = PR "1KLC FREE"; my title
> cpp = cpp; my C prepocessor (whereIsIt)
> include = ; dir to include in my topology file
> define = ;
>
> ;-------------RUN CONTROL---------------------
> integrator = md;
>
> ;--------------OUTPUT CONTROL------------------
> ;TRR outpur
> nstxout = 10000
> nstvout = 10000
> nstfout = 0
>
> ;LOG and EDR output
> nstlog = 10000
> nstenergy = 10000
>
> ;XTC output
> nstxtcout = 1000
> xtc-precision = 1000
>
> ;-------------START TIME & TIMESTEP-----------
> tinit = ; [ps] starting time for your run (only makes
> sense for md, sd, bd integator)
> dt = 0.005 ; [ps] time step for integration (--"--)
> nsteps = 1600000 ; (0) maximum number of steps to integrate
> comm-mode = ; Linear(Remove center of mass
> translation)/Annular(Remove center of mass
> ;translation and rotation)/No(no restriction)
> nstcomm = 1
>
> ;-------------NEIGHBOR SEACHING---------------
>
> nstlist = 5; frequency o update
> neighbor list
> ns_type = grid; make a gid in
> the box and check only
> ;neighboring grid cell when constructing a new neighbor list
> rlist = 1.0; cut-off distance
> for the short-range neighbor list
>
> ;-------------ELECTROSTATICS------------------
> coulombtype = Reaction-field ; reaction field with
> coulomb cut-off rcoulomb
> ; where rcoulomb>rlist. The dielectric constant beyond the cut-off is epsilon_r
> rcoulomb = 1.5 ;distance for the
> coulomb cut-off
> epsilon_rf = 80;dielectric constant
> epsilon_r = 1;
>
> vdwtype = cut-off; twin-range
> cut-off`s with neighbor list cut-off rlist
> ;and VdW cut-off rvdw, where rvdw>rlist
> rvdw = 1.0 ; distance for for
> the LJ or Buckingam cut-off
>
> ;-------------ENERGY MINIMIZATION-------------
> emtol = 200 (kJ/mol*nm); minimisation is converged when
> the maximum force is smaller then this value
> emstep = 0.01; initial step size
>
> ;-------------TEMTERAURE CONTROL--------------
> tcoupl = berendsen
> tc-grps = System
> tau-t = 0.1
> ref-t = 300
>
> ;--------- PRESSURE CONTROL---------------------
> Pcoupl = no
> Pcoupltype = Isotropic
> tau-p = 1
> ref_p = 1
> compressibility = 4.5E-5
>
> ;------------ VELOCITY INITIATION -----------------------
> gen-vel = no
> gen-temp = 300
>
> ;------------- BONDS -----------------------
> constraints = all-bonds
> constraint-algorithm = Lincs
> unconstrained-start = yes
> Shake-SOR = no
> shake-tol = 0.0001
> lincs-order = 8
> lincs-warnangle = 30
> lincs-iter = 8
> morse = no
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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