> > "Not working" is too vague a symptom for anyone to guess what the problem > > is, sorry. > > > > Mark > > On Oct 24, 2013 9:39 AM, "Santu Biswas" <[email protected]> > wrote: > > > > > dear users, > > > > > > I am performing 500ps mdrun in vacuum for > > polypeptide(formed > > > by 10-residues leucine) using gromacs_4.5.5(double- precision) using > > > opls-aa/L force field.Input file for 500ps mdrun is given below > > > > > > > > > title = peptide in vaccum > > > cpp = /lib/cpp > > > > > > ; RUN CONTROL > > > integrator = md > > > comm_mode = ANGULAR > > > nsteps = 500000 > > > dt = 0.001 > > > ; NEIGHBOR SEARCHING > > > nstlist = 0 > > > ns_type = simple > > > pbc = no > > > rlist = 0 > > > ; OUTPUT CONTROL > > > nstxout = 1000 > > > nstvout = 1000 > > > nstxtcout = 0 > > > nstlog = 1000 > > > constraints = none > > > nstenergy = 1000 > > > ; OPTION FOR ELECTROSTATIC AND VDW > > > rcoulomb = 0 > > > ; Method for doing Van der Waals > > > rvdw = 0 > > > ; OPTIONS FOR WEAK COUPLING ALGORITHMS > > > tcoupl = V-rescale > > > tc_grps = Protein > > > tau_t = 0.1 > > > ref_t = 300 > > > gen_vel = yes > > > gen_temp = 300 > > > > > > Using the 500ps trajectory if i run g_hbond_d for calculating the > number > > of > > > hydrogen bonds as a function of time using index file(where atom O and > > atom > > > N H is used) it is not working. > > > Also if i used g_rdf_d with pbc=no using the 500ps trajectory it is > also > > > not working. > > > I do not know why this is happening. > > > > > > ------ > > > santu > > > -- > > Thanks Mark for your reply. > > > > Using the 500ps trajectory i want to calculate the number of hydrogen > bonds as a function of time in vacuum .For this calculation i > > > have uesd > > g_hbond_d -f traj_0-500ps.trr -s 500ps.tpr -n index.ndx -num > > hbond-num.xvg -dist dist.xvg -ang angle.xvg > > With what groups? Can there be any hydrogen bonds between those groups?
Is there a bug fixed in a version of g_hbond that isn't 2 years old? Did a shorter trajectory work because it took less time? Does doing only one of three analyses help things to work? You'd be much closer to a solution if you'd tried some simplifications and done some detective work already ;-) > > Programm was running .After 1 hour it was still running but there was no > > output. > > > > If I calculate the number of hydrogen bonds as a function of time in > water (no vacuum) using the same command line then there was no problem. > > Same problem when I used g_rdf in vacuum.The commad line I have used > g_rdf_4.5.5 -f traj.trr -s 500ps.tpr -n index.ndx -o rdf.xvg and also > checked with -nopbc with the same command line. > RDF of what, in vacuum? What groups did you use? > The programm is running but in the output file nothing is written. > If I used g_rdf in water using the same command line there was no > problem. > OK - but does your analysis make sense in vacuum? Mark Thanks Mark for your reply In the index file I mentioned C=O oxygen atom and N-H hydrogen atom. Now I want to calculate the distance between O atom and N-H hydrogen atom using g_rdf in vacuum. Similarly using the same index file I want to calculate the number of hydrogen bonds as a function of time in vacuum using g_hbond. Yes there is a H bond between C=O oxygen atom of i-th residue and N-H hydrogen of i+4-th residue. I also checked with shorter trajectory there is also same problem . Please let me know If there are any mistakes. ----- santu -- gmx-users mailing list [email protected] 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. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
