Hello Chris, I followed the steps as mentioned in the umbrella sampling tutorial in gromacs.
After NPT equilibration step, i did the umbrella simulation runs. Below are the commands which i used: grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -n index.ndx -o umbrella0.tpr mdrun -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg -s umbrella0.tpr -o 0.cpt -c 0.gro -x 0.xtc So, I had 24 such commands in my job submission script (one script i had all the grompp command and in other script i had mdrun command) for 24 windows, which gave me 24 cpt files. After the final 24th window run, along with the output names specified by me it also outputted default gromacs file names state_prev.cpt, state.cpt, md.log, ener.edr. Please can I know if its necessary to output even log files for these 24 windows. Size of the state.cpt or the other cpt files which i got during npt equilibration are 1.2 MB (these cpt files are okie when i do gmxcheck, it does not give any error), where as of 24 different cpt files, each has file size of 715MB. I had run simulations for 10ns on each window. Kind Regards, chetan ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of chris.ne...@utoronto.ca [chris.ne...@utoronto.ca] Sent: 20 September 2011 13:37 To: gmx-users@gromacs.org Subject: [gmx-users] check point file corrupted - umbrella sampling I am somewhat confused. When I do umbrella sampling, I use a bash script to set up a number of separate restrained simulations. Thus I would get one .cpt file for each simulation. What are you doing that in addition to these .cpt files you also get a state.cpt and state_perv.cpt? Perhaps you had better start at the beginning and explain what you did. Nevertheless, if your .cpt file is indeed corrupt, then you can not use it. You must extract a .gro from the final frame and use it (along with your .trr and .edr if you like) to generate a new .tpr file that will start a new run from where you left off. Chris. -- original message -- Hello Chris, Thank you very much for your reply. I have done following test as you suggested to check whether the checkpoint file are corrupted. 1) Yes, I have used same version of gromacs for mdrun and to produce .cpt file. 2) when i do gmxcheck -f 0.cpt # i get the same error. Fatal error: Start of file magic number mismatch, checkpoint file has 1993, should be 171817 The checkpoint file is corrupted or not a checkpoint file 3) When I do mdrun -s umbrella0.tpr # it runs without any error. 4) My mdruns has not outputted anything like 0_prev.cpt, i just have 0.cpt. I had run US for 24 windows, each for 10ns and produced 24 different cpt files. Along with these 24 different .cpt files, in the end it also produced state.cpt and state_prev.cpt. When i did gmxcheck -f state.cpt # i get Checking file state.cpt # Atoms 51895 Last frame -1 time 10000.000 Item #frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 When i did gmxcheck -f state_prev.cpt # i get Checking file state_prev.cpt # Atoms 51895 Last frame -1 time 9730.730 Item #frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 I just have only one md.log file in the end, i haven't outputted md.log file for each window. Kind Regards, Chetan. ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Chris Neale [chris.ne...@utoronto.ca] Sent: 19 September 2011 17:59 To: gmx-users@gromacs.org Subject: [gmx-users] check point file corrupted - umbrella sampling I have used tpbconv -until to extend a US simulation without error, and I assume that tpbconv -extend is also fine for US simulations. 1. Are you using the same version of gromacs mdrun as you used to produce your .cpt file initially? 2. what happens when you run gmxcheck on the .cpt file? 3. what happens when you run mdrun with the umbrella0.tpr file? 4. what happens when you use 0_prev.cpt? What I am getting at is that you have stated that the checkpoint file is corrupted in your subject line, but you have not provided any evidence of that. I do appreciate that you have pasted your exact commands. The next step is to see if there is any way to test your hypothesis that the checkpoint file is corrupted. Chris. -- original message -- Hi, I am using Gromacs 4.5.3 and want to extend my umbrella sampling runs. But i get an errror while running the "mdrun" step of extension command, saying "Start of file magic number mismatch, checkpoint file has 1993, should be 171817. The checkpoint file is corrupted or not a checkpoint file" Below are the commands I have used to run the umbrella sampling run grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -n index.ndx -o umbrella0.tpr mdrun -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg -s umbrella0.tpr -o 0.cpt -c 0.gro -x 0.xtc I used the below commands for extension: tpbconv -s umbrella0.tpr -extend 20000 -o umbrella_new.tpr mdrun -s umbrella_new.tpr -cpi 0.cpt -pf pullf-umbrella_new.xvg -px pullx-umbrella_new.xvg -o new.cpt -c new.gro -x new.xtc (at this step i get the error) I have not touched the cpt files. Its the same as it was outputed. Please can I know what might have gone wrong. Kind Regards, chetan -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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