[gmx-users] Extending a run for different number of nodes
DimitryASuplatov
genesup at gmail.com
Mon Sep 15 10:24:35 CEST 2008
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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