[gmx-users] Extending a run for different number of nodes
Vasilii Artyukhov
darth.vasya at gmail.com
Mon Sep 15 10:28:49 CEST 2008
grompp -c .trr -e .edr should do it
2008/9/15 DimitryASuplatov <genesup at gmail.com>
> Thank you for your answer.
> I think that it would be better if I simply rephrase my question -
> I have an gro/top/itc stuff for the initial structure, tpr gerenated for
> 8 nodes and trr/xtc run for 10ns. How could I extend this run for
> another 5 ns but this time to run on 4 nodes.
> Thank you.
> SDA
>
>
> >
> > 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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> > >
> >
>
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