HI<div> </div><div> I want to run my system for almost 50 ns but as diskspace becomes almost full to run system for this much time </div><div> so which of the option u suggest</div><div> 1. Giving 10ns with each run by .mdp option .</div>
<div> 2. giving full run of 50ns and then creating at each time new tpr file to continue run for next step while storing .xtc </div><div> at each step and concurrent removal of .trr file as it occupies a lots of diskspace.</div>
<div><br></div><div> While restarting run by using tpbconv to create new .tpr file for new run may i know following of which commond is </div><div> correct</div><div><br></div><div> 1. tpbconv -s md1_out.tpr -o md2_out.tpr -e md1_out.edr</div>
<div> 2 tpbconv -s md1_out.tpr -o md2_out.tpr -e md1_out.edr -extend 8000.</div><div> tell me what -extends signifies i.e.point from where you want to continue or extend the given number of steps.</div>
<div> im asking this because when i run it using previous (1) commend i got run in which the middle portion was </div><div> containing no information about run. </div><div> that is system run well till 7 ns then i killed run to continue it for seond time this time it run well but at the end </div>
<div> i found that 7ns - 13ns portin was not there, why it is so?</div><div> ( may it be the reason because some incomplete frames are present .)</div><div> </div><div> also </div><div> tell me which is the best way to check whether the system is running well or not .?</div>
<div> </div><div> regarding g_rms</div><div> While selecting groups for RMSD which is correct </div><div> 1. select whole system with solvent</div><div> 2. select only molecule of interest .</div><div>
also while choosing groups is it correct to choose both time i.e. for least square fitting and RMSD same groups.</div><div><br></div><div> Thanking you in Advance.</div><div><br></div><div> Mr. Pavan Payghan</div>
<div> INDIAN INSTITUTE OF CHEMICAL BIOLOGY </div><div> KOLKATA</div><div> </div>