<div dir="ltr">grompp -c .trr -e .edr should do it<br><br><div class="gmail_quote">2008/9/15 DimitryASuplatov <span dir="ltr"><<a href="mailto:genesup@gmail.com">genesup@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Thank you for your answer.<br>
I think that it would be better if I simply rephrase my question -<br>
I have an gro/top/itc stuff for the initial structure, tpr gerenated for<br>
8 nodes and trr/xtc run for 10ns. How could I extend this run for<br>
another 5 ns but this time to run on 4 nodes.<br>
Thank you.<br>
SDA<br>
<div><div></div><div class="Wj3C7c"><br>
<br>
><br>
> DimitryASuplatov wrote:<br>
> > Hello,<br>
> > I have completed a 10ns run. Now I want to extend it to 20ns. The<br>
> > problem is that the initial tpr was compiled for 8 processors and now<br>
> > I have only 4 cores.<br>
> > What I tried to do is used tpbconv to make a 10ns extended tpr, then<br>
> > used an exactly the same mdp file to grompp it all together with -np 4<br>
> > to a new tpr file.<br>
><br>
> What do you mean "grompp it all together?" It sounds like you are trying to use<br>
> both tpbconv and grompp for some reason. The only way to change the number of<br>
> processors is to use grompp, not tpbconv, providing it your .trr and .edr files<br>
> with the -t and -e flags.<br>
><br>
> > The problem is that at the beginning of the trajectory the structure<br>
> > is undergoing a structural change with 0.12 nm from the initial<br>
> > structure. That means that the structure is actually relaxed and that<br>
> > is not something I want to see.<br>
><br>
> How do you know this is not the normal behavior?<br>
><br>
> -Justin<br>
><br>
> > I have used this in my mdp<br>
> > ;------------ VELOCITY INITIATION -----------------------<br>
> > gen-vel = no<br>
> > gen-temp = 300<br>
> ><br>
> > That means that no velocities were generated and I expect to see no<br>
> > relaxation but the continuation of my run.<br>
> ><br>
> > What am I doing wrong? How to extend a run without relaxation.<br>
> > Thank you. I appreciate any help.<br>
> > SDA<br>
> ><br>
> > My mdp file is the following.<br>
> > ;-------------PREPROCESSING OPTIONS------------<br>
> > title = PR "1KLC FREE"; my title<br>
> > cpp = cpp; my C prepocessor (whereIsIt)<br>
> > include = ; dir to include in my topology file<br>
> > define = ;<br>
> ><br>
> > ;-------------RUN CONTROL---------------------<br>
> > integrator = md;<br>
> ><br>
> > ;--------------OUTPUT CONTROL------------------<br>
> > ;TRR outpur<br>
> > nstxout = 10000<br>
> > nstvout = 10000<br>
> > nstfout = 0<br>
> ><br>
> > ;LOG and EDR output<br>
> > nstlog = 10000<br>
> > nstenergy = 10000<br>
> ><br>
> > ;XTC output<br>
> > nstxtcout = 1000<br>
> > xtc-precision = 1000<br>
> ><br>
> > ;-------------START TIME & TIMESTEP-----------<br>
> > tinit = ; [ps] starting time for your run (only makes<br>
> > sense for md, sd, bd integator)<br>
> > dt = 0.005 ; [ps] time step for integration (--"--)<br>
> > nsteps = 1600000 ; (0) maximum number of steps to integrate<br>
> > comm-mode = ; Linear(Remove center of mass<br>
> > translation)/Annular(Remove center of mass<br>
> > ;translation and rotation)/No(no restriction)<br>
> > nstcomm = 1<br>
> ><br>
> > ;-------------NEIGHBOR SEACHING---------------<br>
> ><br>
> > nstlist = 5; frequency o update<br>
> > neighbor list<br>
> > ns_type = grid; make a gid in<br>
> > the box and check only<br>
> > ;neighboring grid cell when constructing a new neighbor list<br>
> > rlist = 1.0; cut-off distance<br>
> > for the short-range neighbor list<br>
> ><br>
> > ;-------------ELECTROSTATICS------------------<br>
> > coulombtype = Reaction-field ; reaction field with<br>
> > coulomb cut-off rcoulomb<br>
> > ; where rcoulomb>rlist. The dielectric constant beyond the cut-off is epsilon_r<br>
> > rcoulomb = 1.5 ;distance for the<br>
> > coulomb cut-off<br>
> > epsilon_rf = 80;dielectric constant<br>
> > epsilon_r = 1;<br>
> ><br>
> > vdwtype = cut-off; twin-range<br>
> > cut-off`s with neighbor list cut-off rlist<br>
> > ;and VdW cut-off rvdw, where rvdw>rlist<br>
> > rvdw = 1.0 ; distance for for<br>
> > the LJ or Buckingam cut-off<br>
> ><br>
> > ;-------------ENERGY MINIMIZATION-------------<br>
> > emtol = 200 (kJ/mol*nm); minimisation is converged when<br>
> > the maximum force is smaller then this value<br>
> > emstep = 0.01; initial step size<br>
> ><br>
> > ;-------------TEMTERAURE CONTROL--------------<br>
> > tcoupl = berendsen<br>
> > tc-grps = System<br>
> > tau-t = 0.1<br>
> > ref-t = 300<br>
> ><br>
> > ;--------- PRESSURE CONTROL---------------------<br>
> > Pcoupl = no<br>
> > Pcoupltype = Isotropic<br>
> > tau-p = 1<br>
> > ref_p = 1<br>
> > compressibility = 4.5E-5<br>
> ><br>
> > ;------------ VELOCITY INITIATION -----------------------<br>
> > gen-vel = no<br>
> > gen-temp = 300<br>
> ><br>
> > ;------------- BONDS -----------------------<br>
> > constraints = all-bonds<br>
> > constraint-algorithm = Lincs<br>
> > unconstrained-start = yes<br>
> > Shake-SOR = no<br>
> > shake-tol = 0.0001<br>
> > lincs-order = 8<br>
> > lincs-warnangle = 30<br>
> > lincs-iter = 8<br>
> > morse = no<br>
> ><br>
> > sda@leiden:~/klc/MD/free> cat pr_free.extendfrom12to20ns.mdp<br>
> > ;-------------PREPROCESSING OPTIONS------------<br>
> > title = PR "1KLC FREE"; my title<br>
> > cpp = cpp; my C prepocessor (whereIsIt)<br>
> > include = ; dir to include in my topology file<br>
> > define = ;<br>
> ><br>
> > ;-------------RUN CONTROL---------------------<br>
> > integrator = md;<br>
> ><br>
> > ;--------------OUTPUT CONTROL------------------<br>
> > ;TRR outpur<br>
> > nstxout = 10000<br>
> > nstvout = 10000<br>
> > nstfout = 0<br>
> ><br>
> > ;LOG and EDR output<br>
> > nstlog = 10000<br>
> > nstenergy = 10000<br>
> ><br>
> > ;XTC output<br>
> > nstxtcout = 1000<br>
> > xtc-precision = 1000<br>
> ><br>
> > ;-------------START TIME & TIMESTEP-----------<br>
> > tinit = ; [ps] starting time for your run (only makes<br>
> > sense for md, sd, bd integator)<br>
> > dt = 0.005 ; [ps] time step for integration (--"--)<br>
> > nsteps = 1600000 ; (0) maximum number of steps to integrate<br>
> > comm-mode = ; Linear(Remove center of mass<br>
> > translation)/Annular(Remove center of mass<br>
> > ;translation and rotation)/No(no restriction)<br>
> > nstcomm = 1<br>
> ><br>
> > ;-------------NEIGHBOR SEACHING---------------<br>
> ><br>
> > nstlist = 5; frequency o update<br>
> > neighbor list<br>
> > ns_type = grid; make a gid in<br>
> > the box and check only<br>
> > ;neighboring grid cell when constructing a new neighbor list<br>
> > rlist = 1.0; cut-off distance<br>
> > for the short-range neighbor list<br>
> ><br>
> > ;-------------ELECTROSTATICS------------------<br>
> > coulombtype = Reaction-field ; reaction field with<br>
> > coulomb cut-off rcoulomb<br>
> > ; where rcoulomb>rlist. The dielectric constant beyond the cut-off is epsilon_r<br>
> > rcoulomb = 1.5 ;distance for the<br>
> > coulomb cut-off<br>
> > epsilon_rf = 80;dielectric constant<br>
> > epsilon_r = 1;<br>
> ><br>
> > vdwtype = cut-off; twin-range<br>
> > cut-off`s with neighbor list cut-off rlist<br>
> > ;and VdW cut-off rvdw, where rvdw>rlist<br>
> > rvdw = 1.0 ; distance for for<br>
> > the LJ or Buckingam cut-off<br>
> ><br>
> > ;-------------ENERGY MINIMIZATION-------------<br>
> > emtol = 200 (kJ/mol*nm); minimisation is converged when<br>
> > the maximum force is smaller then this value<br>
> > emstep = 0.01; initial step size<br>
> ><br>
> > ;-------------TEMTERAURE CONTROL--------------<br>
> > tcoupl = berendsen<br>
> > tc-grps = System<br>
> > tau-t = 0.1<br>
> > ref-t = 300<br>
> ><br>
> > ;--------- PRESSURE CONTROL---------------------<br>
> > Pcoupl = no<br>
> > Pcoupltype = Isotropic<br>
> > tau-p = 1<br>
> > ref_p = 1<br>
> > compressibility = 4.5E-5<br>
> ><br>
> > ;------------ VELOCITY INITIATION -----------------------<br>
> > gen-vel = no<br>
> > gen-temp = 300<br>
> ><br>
> > ;------------- BONDS -----------------------<br>
> > constraints = all-bonds<br>
> > constraint-algorithm = Lincs<br>
> > unconstrained-start = yes<br>
> > Shake-SOR = no<br>
> > shake-tol = 0.0001<br>
> > lincs-order = 8<br>
> > lincs-warnangle = 30<br>
> > lincs-iter = 8<br>
> > morse = no<br>
> > _______________________________________________<br>
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><br>
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</div></div></blockquote></div><br></div>