Thanks Tsjerk, I am rerunning the simulation with SDS+SOL+IONS in a single tcoupl group. I was trying to anneal because, I suspected huge velocities on the atoms due to a "high starting temperature", well not high enough to be worried and I had done a NVT equilibration already, so shouldn't cause any problems, but I just wanted to be sure. I am running the SDS simulations with water simultaneously... haven't checked its properties yet.
Venky On 4/25/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:
Hi Venky, On 4/25/07, Venky Krishna <[EMAIL PROTECTED]> wrote: > Hi gmx-users, > > System Setup: Looks good > > Problem: Did you check the PRODRG2 derived parameters? Run through the molecule yourself (draw it!). Check the atom, bond, etc. types. Also, run a simulation of only SDS (with water) to check the properties, like the area per lipid, etc. > > Parameters: Won't go through all this... (but thanks for adding it..., makes it a good mail..., I'm just being lazy). > and here are my relevant MD mdp parameters. > tc-grps = Protein SDS SOL Na+ Cl- > tau-t = 0.5 0.5 0.5 0.5 0.5 > ref-t = 300 300 300 300 300 This is BAD BAD BAD! We just dealt with this issue a few times in the past few weeks! It may be the cause of your problem, and you should fix it and rerun the simulation, before turning back to the list. Merge your sodium and chloride with the solvent, so you have three reasonably large groups to couple to the heat bath. Check the archives on this one. > ; SIMULATED ANNEALING > ; Type of annealing for each temperature group (no/single/periodic) > annealing = single single single single single > ; Number of time points to use for specifying annealing in each group > annealing_npoints = 2 2 2 2 2 > ; List of times at the annealing points for each group > annealing_time = 0 20 0 20 0 20 0 20 0 20 > ; Temp. at each annealing point, for each group. > annealing_temp = 0 300 0 300 0 300 0 300 0 300 Is there any specific reason for annealing here? You didn't mention it in your setup. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
-- Venks ~ You will become rich and famous, unless you don't.
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