[gmx-users] doubt

[Nuno R. L. Ferreira]

Hi Smith


If your run crashed, than you want to use the original tpr. Tpbconv will start the next run, where the previous run crashed (using of course the outputs from the crashed run), if the crash was due to system powe failure for e.g.  If the crash was due to MD system problems (pressure scaling, box exploding ...) you have to see where the problem is.

If you want to extend a previous run, with the same mdp parameters, use -extend in tpbconv.

To continue a run, but with some parameters changed, like tau_p, you have to create another tpr.  The starting coordinates will be the ones outputed by the previous run, in your case run1.gro. But, at the final, in IMHO, I think you cannot analyse your traj as run1+run2, cause you changed parameters.  The "experimental" conditions are not the same. Unless you want something else.

Think this commands will do the job:
grompp -f new.mdp -c run1.gro -o new.tpr
mdrun -v -s new.tpr

If I'm incorrect, please correct me.


Regards,
Nuno

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Nuno Ricardo Santos Loureiro da Silva Ferreira
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra - Portugal
Fax: +351 239 827703  - www.biolchem.qui.uc.pt
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  ----- Original Message ----- 
  From: Gsmith1 
  To: gmx-users at gromacs.org 
  Sent: Tuesday, April 20, 2004 10:21 AM
  Subject: [gmx-users] doubt


  dear gromacs users ,
  Iam a very new user to gromacs.I use gromacs-3.2.1.I followed the exact steps given in getting started.html for speptide.I have completed simulation of a protein for 2ns.I want to continue(extend) the simulation for another 3ns and change tautp =1.0 in the mdp file now.From archive mails i learned that tpbconv should be used as,
  I got these outputs from first 2ns run run1.gro, run1.trr,run1.edr.but 

  Iam confused which .tpr file i should use?

  1.Can I use the .tpr (created using grompp with  afterminim.gro) for mdrun (first 2ns) or should i use run1.gro file of just finished output of mdrun for 2ns for grompp ,change timesteps,other options ,create a new.tpr and then use this .tpr for tpbconv as ,

  *tpbconv -f run1.trr -s new.tpr -e run1.edr -o restart.tpr -extend 3000
  *mdrun -v -s restart.tpr -o -e 

  Iam confused to which tpr should i use.please anyone tell whats exact  protocol.thanks -smith  



   
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