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Hi,<br><br>In this manner you use the same random seed and thus noise for all parts.<br>In most cases this will not lead to serious artifacts with SD,<br>but you can never be sure.<br>When checkpoints are used, you do not repeat random numbers.<br>This also gives a difference between serial and parallel in 4.0.<br>With serial you get exactly the same noise per atom, in parallel not,<br>since atoms migrate from one node to another (with domain decompostion).<br><br>If you do not use checkpoints, use ld_seed=-1 and do not use tpbconv.<br><br>Berk<br><br><br>> Date: Wed, 4 Feb 2009 15:05:47 -0500<br>> From: chris.neale@utoronto.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] micelle disaggregated in serial, but not parallel, runs using sd integrator<br>> <br>> Thank you Berk,<br>> <br>> I will loon into tau_t=1.0 (or at least not = 0.1). Thank you for the hint.<br>> <br>> These simulations run in 200 ps segments and utilize restarts via <br>> grompp -t -e like this:<br>> <br>> EXECUTING: <br>> /hpf/projects1/pomes/cneale/exe/gromacs-4.0.3/exec/bin/grompp -f <br>> /scratch/4772976.1.ompi-4-21.q/md6_running/dpc50_md6.mdp -c <br>> md5_success/dpc50_md5.gro -p dpc50.top -n dpc50.ndx -o <br>> /scratch/4772976.1.ompi-4-21.q/md6_running/dpc50_md6.tpr -maxwarn 1 -t <br>> md5_success/dpc50_md5.trr -e md5_success/dpc50_md5.edr<br>> <br>> The -maxwarn 1 is to avoid this message:<br>> <br>> WARNING 1 [file <br>> /scratch/4772976.1.ompi-4-21.q/md5_running/dpc50_md5.mdp, line unknown]:<br>> Can not couple a molecule with free_energy = no<br>> <br>> which I don't think should be a problem.<br>> <br>> ###<br>> <br>> I didn't check temperatures previously, but I did check the energy <br>> components output the the .log file in zero step mdruns in both serial <br>> and parallel and found no difference.<br>> <br>> Here is the information on temperature and total energy for the serial <br>> and parallel runs:<br>> <br>> For the run in parallel:<br>> <br>> Last energy frame read 780 time 7800.000<br>> <br>> Statistics over 1950001 steps [ 0.0000 thru 7800.0000 ps ], 1 data sets<br>> All averages are exact over 1950001 steps<br>> <br>> Energy Average RMSD Fluct. Drift <br>> Tot-Drift<br>> -------------------------------------------------------------------------------<br>> Temperature 303.322 901.905 901.905 -6.34952e-06 <br>> -0.0495263<br>> Heat Capacity Cv: -1.01712 J/mol K (factor = 8.84124)<br>> <br><br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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