Re: [gmx-users] Continuation of Serial MD simulation in Parallel

[Sridhar Acharya]

Thanks so much for the answer. I have one more doubt. Could you please answer? I could make the change and run, but still the following line in the log file, "Starting time for run is 0 ps" (BLUE color), appears controversial to me. The log message is as follows. ###################################################### Checking consistency between energy and charge groups... getting data from old trajectory ... Reading Coordinates, Velocities and Box size from old trajectory Will read till time 20000 trn version: GMX_trn_file Reading frame      60 time 19917.312   Using frame at t = 20000 ps Starting time for run is 0 ps Calculating fourier grid dimensions for X Y Z Using a fourier grid of 72x56x75, spacing 0.111 0.114 0.117 splitting topology... Walking down the molecule graph to make shake-blocks There are 14390 charge group borders and 12308 shake borders There are 12308 total borders Division over nodes in atoms:  10455 10455 10455 10455 writing run input file... ############################################################### Dallas B. Warren wrote: So I am generating .tpr file as follows using the command as follows. Does the log message (Highlighted in RED) "Velocities generated: ignoring velocities in input trajectory", means that the simulation wont be continuation of the earlier one? That warning tells you that in your .mdp file you have velocity generation on, turn that option off. You don't want that if you want a continuation of the run. The velocity of the atoms is taken from the .trr file that you feed to grompp. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. -- Sridhar Acharya, M Senior Research Fellow Lab of Computational Biology CDFD, Gandipet Campus Hyderabad. AP. INDIA http://www.cdfd.org.in email: [EMAIL PROTECTED] Phone: Lab: 08413-235467*2044 Mobile: 9866147193

begin:vcard
fn:Sridhar Acharya
n:Acharya;Sridhar
org:CDFD;Computational Biology
adr:;;Gandipet Campus;Hyderabad;AP;;INDIA
email;internet:[EMAIL PROTECTED]
title:Senior Research Fellow
tel;work:08413-235467*2044
tel;home:040-27505833
tel;cell:9866147193
x-mozilla-html:TRUE
url:http://www.cdfd.org.in
version:2.1
end:vcard


_______________________________________________
gmx-users mailing list    gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php