Re: [gmx-users] genion doubt
HI I'm not sure about this kind of error but as per my knowledge the problem might be with the parameter cpp in mdp file. In my mdp file it is as follows title = ecoli_nusG cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.001 ; ps ! nsteps = 10 ; total 100 ps. nstcomm = 1 .. .. and somewhere i read the nsteps should be between 5-10 for pr dynamics. search gromacs tutorial for better clue... [?] On Sat, May 15, 2010 at 6:03 AM, manjula kasinathan wrote: > > hi snip > > Thank u. as per ur suggestion i added sodium ions to my protein. > then i carried out mdrun for energy minimization nsteps 3000 but i runs only > for 1108 steps. then i went to position restrain steps the command i gave > > grompp -f pr.mdp -c em.gro -p top.top -o pr.tpr > > i got a fatal error > Too many warnings (1), grompp terminated. > If you are sure all warnings are harmless, use the -maxwarn > option > > WARNING 1 [file pr.mdp, line unknown]: > Unknown or double left-hand 'warnings' in parameter file > > y i'm getting this error.how can i correct this could any one help plz. > > my pr.mdp file > > title = FWS > warnings= 10 > cpp = /usr/local/gromacs/share/gromacs/cpp > define = -DPOSRES > constraints = all-bonds > integrator = md > dt = 0.002 ; ps ! > nsteps = 500 ; total 1.0 ps. > nstcomm = 1 > nstxout = 250 ; collect data every 0.5 ps > nstvout = 1000 > nstfout = 0 > nstlog = 10 > nstenergy = 10 > nstlist = 10 > ns_type = grid > rlist = 1.0 > coulombtype = PME > rcoulomb= 1.0 > vdwtype = cut-off > rvdw= 1.4 > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = 1e-5 > optimize_fft= yes > ; Berendsen temperature coupling is on > Tcoupl = v-rescale > tau_t = 0.1 0.1 > tc-grps = protein non-protein > ref_t = 300 300 > ; Pressure coupling is on > Pcoupl = parrinello-rahman > Pcoupltype = isotropic > tau_p = 0.5 > compressibility = 4.5e-5 > ref_p = 1.0 > ; Generate velocites is on at 300 K. > gen_vel = yes > gen_temp= 300.0 > gen_seed= 173529 > > with this warnings i proceeded with mdrun but i get the following LINCS > warnnings > > starting mdrun 'Protein in water' > 500 steps, 1.0 ps. > step 300, will finish Sat May 15 08:57:23 2010 > Step 394, time 0.788 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.000103, max 0.001028 (between atoms 4478 and 4480) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length >4478 4480 33.40.1081 0.1091 0.1090 > Step 423, time 0.846 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.442275, max 40.666431 (between atoms 8211 and 8212) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length >8473 8476 88.60.1527 0.2741 0.1522 >8473 8475 89.90.1094 3.6185 0.1090 >8473 8474 89.50.1094 0.2778 0.1090 >8471 8473 87.20.1455 0.2548 0.1449 >8471 8472 33.20.1013 0.1241 0.1010 >8215 8217 32.80.1090 0.1240 0.1090 >8215 8216 39.20.1091 0.1282 0.1090 >8211 8215 45.80.1536 0.1603 0.1529 >8211 8213 44.00.1425 0.1645 0.1410 >8211 8212 90.20.4225 4.5416 0.1090 >8209 8211 45.60.1511 0.1348 0.1529 >8209 8210 32.40.1098 0.1199 0.1090 >8207 8209 33.30.1482 0.1823 0.1449 >7224 7225 30.40.1013 0.1010 0.1010 >5296 5297 30.50.1093 0.1092 0.1090 > Warning: 1-4 interaction between 8208 and 8213 at distance 4.720 which is > larger than the 1-4 table size 2.400 nm > These are ignored for the rest of the simulation > This usually means your system is exploding, > if not, you should increase table-extension in your mdp file > or with user tables increase the table size > > Step 424, time 0.848 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 171806.092017, max 19412182.00 (between atoms 8235 and 8236) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length >8507 8508 90.00.1011 0.2179 0.1010 >8497 8499 39.80.1460 0.2065 0.1449 >8497 8498 59.80.1009 0.1923 0.1010 >8495 8497 44.00.1354 729.7847 0.1335 >8495 8496 94.40.123
Re: [gmx-users] rmsd between different monomers
you said you have used online server for superimposition ... which one you used... try TOPMATCH server On Sun, May 9, 2010 at 5:31 PM, Anupam Nath Jha wrote: > > Ok. > > But when I run this command > g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out > > it ask me groups... and that i thought is for fitting/// > > for example - > > > Select group for least squares fit > Group 0 (C-alpha_chain1) has 249 elements > Group 1 (C-alpha_chain2) has 249 elements > Group 2 (C-alpha_chain3) has 249 elements > Group 3 (C-alpha_chain4) has 249 elements > Select a group: 0 > Selected 0: 'C-alpha_chain1' > Select group for RMSD calculation > Group 0 (C-alpha_chain1) has 249 elements > Group 1 (C-alpha_chain2) has 249 elements > Group 2 (C-alpha_chain3) has 249 elements > Group 3 (C-alpha_chain4) has 249 elements > Select a group:1 > Selected 1: 'C-alpha_chain2' > > - > > Is it not superimposing these two chins and calculating RMSD between > them??? > > -- > anupam > > > > On 9/05/2010 9:29 PM, Justin A. Lemkul wrote: > >> > >> > >> Anupam Nath Jha wrote: > > Anupam Nath Jha wrote: > > Dear all > > > > I made an index file with 4 different groups for 4 different chains > > (since my > > protein is a tetramer) and then run > > > > g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out > > > > to get the rmsd between two different monomers from the same > structure, > > it asked me two different groups and I gave 0 and 1. > > > > The output file is like this > > > > # g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o New > > # > > # g_rms is part of G R O M A C S: > > # > > # Grunge ROck MAChoS > > # > > @ title "RMSD" > > @ xaxis label "Time (ps)" > > @ yaxis label "RMSD (nm)" > > @TYPE xy > > @ subtitle "C-alpha_chain2 after lsq fit to C-alpha_chain1" > > 0.000 0.001 > > > In the command you've given (with the same file for -s and -f), > you're computing > the RMSD at time zero, after fitting to the structure at time zero, > so the RMSD > must be zero. > >>> > >>> > >>> but I am giving different groups (as chains). I am trying to get RMSD > >>> between > >>> two monomers in same structure so what's wrong in that > >>> > >> > >> It doesn't matter. The structure for calculation (-f) and the reference > >> structure (-s) are identical, so the RMSD has to be zero, regardless of > >> the fitting group and calculation groups chosen. > > > > Exactly. Only if you can fit group A from one file to group B from a > > file (which may or may not be the same file) can Anupam do this > > calculation. g_rms seems not to allow this. > > > > Instead, Anupam should use trjconv or editconf to select groups > > beforehand, as I think I suggested a few days back. Thus (say) editconf > > produces file_with_group_A.pdb and editconf produces > > file_with_group_B.pdb, which allows g_rms -f file_with_group_A -s > > file_with_group_B. This will work if the two groups have the same atoms > > in matching orders, which should be the case for a tetramer setup. > > > > Mark > > > > so the rmsd = 0.001 > > > > whereas when I use online server it gives me 1.4. > > > > so what am I doing wrong? > > > Then whatever you're giving the online server is different. The > Gromacs > calculation seems to be correct. > > -Justin > > >>> > >>> > >>> > > regrads > > anupam > > > > > > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > > >>> > >>> > >> > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.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 gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mail
[gmx-users] To calculate surface area of of simulated protein
Hello gmx users.. Can anybody tell me is there any possibility to calculate the surface area of the protein before and after the simulation. waiting for u'r reply.. -- Bharath.K.Chakravarthi Ph:9535629260 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Finishing time donot showing
that means generating a trajectory file for every 10 steps rite then i may need more disk space On Tue, Apr 20, 2010 at 11:41 PM, XAvier Periole wrote: > > On Apr 20, 2010, at 7:39 PM, Bharath.K. Chakravarthi wrote: > > no i did not used -v flag at that command may be thats the mistake > thank u Justin > > On Tue, Apr 20, 2010 at 10:54 PM, Justin A. Lemkul wrote: > >> >> >> Bharath.K wrote: >> >>> I'm using gromacs-3.3.3 and here is the parameter >>> >>> .. >>> .. >>> nstxout = 500 >>> nstvout = 1000 >>> nstfout = 0 >>> nstlist = 100 >>> >> This might not be the best choice! it is generally kept under 10! It > depends on your > system/force field though > > nstlog = 100 >>> nstenergy = 10 >>> nstxtcout = 500 >>> .. >>> .. >>> >>> for writing trajectories in .mdp file and what is check point file and >>> -cpi file.cpt ... >>> i did not get u :( >>> >>> >> This is why stating your Gromacs version at the outset is useful. >> Checkpointing was introduced in Gromacs 4.0, so you won't be able to use >> it. >> >> You also have not answered my first question. What is your mdrun command >> line? Did you use the -v flag? If not, you will not get any information >> about completion time. There is nothing that the .mdp options or tpbconv >> will do for you as far as completion time is concerned. >> >> -Justin >> >> >> On Tue, 20 Apr 2010 22:20:35 +0530, XAvier Periole >>> wrote: >>> >>> >>>> >>>>> >tpbconv -s md.tpr -f md_traj.chk.trr -o md_01.tpr -until 1000 >>>>> this shows last step before crashing and starts from there until 1000 >>>>> >>>>> >>>> then >>>>> >>>>> >mdrun -s md_01.tpr -o md_traj_01.trr -c minim_water.gro -g md.log - >>>>> e minim_ener_01.edr >>>>> >>>>> >>>> Nothing seem particularly wrong! May be you write your trajectory file >>>> too often! Did the original the indicated the same amount of data to be >>>> written? >>>> >>>> which version of gmx you are using? actually using the check point >>>> file is relatively easy (-cpi fie.cpt to add to mdrun) and does all >>>> the work for you! >>>> >>>>> >>>>> >>>> >>>> >>>>> On Tue, Apr 20, 2010 at 7:50 PM, XAvier Periole >>>>> wrote: >>>>> >>>>> On Apr 20, 2010, at 9:14 AM, Bharath.K wrote: >>>>> >>>>> Hello all >>>>> i got a system crash at some steps.. >>>>> after creating the new .trr file using command tpbconv >>>>> trr file with tpbconv? you mean tpr? >>>>> and running MDS >>>>> what is MDS? >>>>> >>>>> by mdrun command the approximate finishing time is not showing. >>>>> and also a warning is showing as >>>>> >>>>> WARNING: this run may generate approximately 4583292 Mb of data >>>>> That is a bit enormous >>>>> >>>>> >>>>> is there any changes that i should do while giving the command and >>>>> can i continue with this warning. >>>>> Which exact command did you use? >>>>> >>>>> >>>>> >>>>> -- >>>>> Bharath.K >>>>> Ph-9535629260 >>>>> -- >>>>> gmx-users mailing listgmx-users@gromacs.org >>>>> http://lists.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 thewww >>>>> interface or send it to gmx-users-requ...@gromacs.org. >>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>>> >>>>> -- >>>>> gmx-users mailing listgmx-users@gromacs.org >>>>> http://lists.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 thewww >&g
Re: [gmx-users] Finishing time donot showing
and XAvier [?] On Tue, Apr 20, 2010 at 11:09 PM, Bharath.K. Chakravarthi < bharath.chakravar...@gmail.com> wrote: > no i did not used -v flag at that command may be thats the mistake > thank u Justin > > On Tue, Apr 20, 2010 at 10:54 PM, Justin A. Lemkul wrote: > >> >> >> Bharath.K wrote: >> >>> I'm using gromacs-3.3.3 and here is the parameter >>> >>> .. >>> .. >>> nstxout = 500 >>> nstvout = 1000 >>> nstfout = 0 >>> nstlist = 100 >>> nstlog = 100 >>> nstenergy = 10 >>> nstxtcout = 500 >>> .. >>> .. >>> >>> for writing trajectories in .mdp file and what is check point file and >>> -cpi file.cpt ... >>> i did not get u :( >>> >>> >> This is why stating your Gromacs version at the outset is useful. >> Checkpointing was introduced in Gromacs 4.0, so you won't be able to use >> it. >> >> You also have not answered my first question. What is your mdrun command >> line? Did you use the -v flag? If not, you will not get any information >> about completion time. There is nothing that the .mdp options or tpbconv >> will do for you as far as completion time is concerned. >> >> -Justin >> >> >> On Tue, 20 Apr 2010 22:20:35 +0530, XAvier Periole >>> wrote: >>> >>> >>>> >>>>> >tpbconv -s md.tpr -f md_traj.chk.trr -o md_01.tpr -until 1000 >>>>> this shows last step before crashing and starts from there until 1000 >>>>> >>>>> >>>> then >>>>> >>>>> >mdrun -s md_01.tpr -o md_traj_01.trr -c minim_water.gro -g md.log - >>>>> e minim_ener_01.edr >>>>> >>>>> >>>> Nothing seem particularly wrong! May be you write your trajectory file >>>> too often! Did the original the indicated the same amount of data to be >>>> written? >>>> >>>> which version of gmx you are using? actually using the check point >>>> file is relatively easy (-cpi fie.cpt to add to mdrun) and does all >>>> the work for you! >>>> >>>>> >>>>> >>>> >>>> >>>>> On Tue, Apr 20, 2010 at 7:50 PM, XAvier Periole >>>>> wrote: >>>>> >>>>> On Apr 20, 2010, at 9:14 AM, Bharath.K wrote: >>>>> >>>>> Hello all >>>>> i got a system crash at some steps.. >>>>> after creating the new .trr file using command tpbconv >>>>> trr file with tpbconv? you mean tpr? >>>>> and running MDS >>>>> what is MDS? >>>>> >>>>> by mdrun command the approximate finishing time is not showing. >>>>> and also a warning is showing as >>>>> >>>>> WARNING: this run may generate approximately 4583292 Mb of data >>>>> That is a bit enormous >>>>> >>>>> >>>>> is there any changes that i should do while giving the command and >>>>> can i continue with this warning. >>>>> Which exact command did you use? >>>>> >>>>> >>>>> >>>>> -- >>>>> Bharath.K >>>>> Ph-9535629260 >>>>> -- >>>>> gmx-users mailing listgmx-users@gromacs.org >>>>> http://lists.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 thewww >>>>> interface or send it to gmx-users-requ...@gromacs.org. >>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>>> >>>>> -- >>>>> gmx-users mailing listgmx-users@gromacs.org >>>>> http://lists.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 thewww >>>>> interface or send it to gmx-users-requ...@gromacs.org. >>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>>> >>>>> >>>>> >>>>> -- >>&g
Re: [gmx-users] Finishing time donot showing
no i did not used -v flag at that command may be thats the mistake thank u Justin On Tue, Apr 20, 2010 at 10:54 PM, Justin A. Lemkul wrote: > > > Bharath.K wrote: > >> I'm using gromacs-3.3.3 and here is the parameter >> >> .. >> .. >> nstxout = 500 >> nstvout = 1000 >> nstfout = 0 >> nstlist = 100 >> nstlog = 100 >> nstenergy = 10 >> nstxtcout = 500 >> .. >> .. >> >> for writing trajectories in .mdp file and what is check point file and >> -cpi file.cpt ... >> i did not get u :( >> >> > This is why stating your Gromacs version at the outset is useful. > Checkpointing was introduced in Gromacs 4.0, so you won't be able to use > it. > > You also have not answered my first question. What is your mdrun command > line? Did you use the -v flag? If not, you will not get any information > about completion time. There is nothing that the .mdp options or tpbconv > will do for you as far as completion time is concerned. > > -Justin > > > On Tue, 20 Apr 2010 22:20:35 +0530, XAvier Periole >> wrote: >> >> >>> >tpbconv -s md.tpr -f md_traj.chk.trr -o md_01.tpr -until 1000 this shows last step before crashing and starts from there until 1000 >>> then >mdrun -s md_01.tpr -o md_traj_01.trr -c minim_water.gro -g md.log - e minim_ener_01.edr >>> Nothing seem particularly wrong! May be you write your trajectory file >>> too often! Did the original the indicated the same amount of data to be >>> written? >>> >>> which version of gmx you are using? actually using the check point >>> file is relatively easy (-cpi fie.cpt to add to mdrun) and does all >>> the work for you! >>> >>> >>> On Tue, Apr 20, 2010 at 7:50 PM, XAvier Periole wrote: On Apr 20, 2010, at 9:14 AM, Bharath.K wrote: Hello all i got a system crash at some steps.. after creating the new .trr file using command tpbconv trr file with tpbconv? you mean tpr? and running MDS what is MDS? by mdrun command the approximate finishing time is not showing. and also a warning is showing as WARNING: this run may generate approximately 4583292 Mb of data That is a bit enormous is there any changes that i should do while giving the command and can i continue with this warning. Which exact command did you use? -- Bharath.K Ph-9535629260 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Bharath.K.Chakravarthi Ph:9535629260 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> >> >> > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Bharath.K.Chakravarthi Ph:9535629260 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Finishing time donot showing
Sorry MDS means MD simulation the commands are as follows >tpbconv -s md.tpr -f md_traj.chk.trr -o md_01.tpr -until 1000 this shows last step before crashing and starts from there until 1000 then >mdrun -s md_01.tpr -o md_traj_01.trr -c minim_water.gro -g md.log -e minim_ener_01.edr On Tue, Apr 20, 2010 at 7:50 PM, XAvier Periole wrote: > > On Apr 20, 2010, at 9:14 AM, Bharath.K wrote: > > Hello all >> i got a system crash at some steps.. >> after creating the new .trr file using command tpbconv >> > trr file with tpbconv? you mean tpr? > >> and running MDS >> > what is MDS? > > by mdrun command the approximate finishing time is not showing. >> and also a warning is showing as >> >> WARNING: this run may generate approximately 4583292 Mb of data >> > That is a bit enormous > > >> is there any changes that i should do while giving the command and can i >> continue with this warning. >> > Which exact command did you use? > > >> >> -- >> Bharath.K >> Ph-9535629260 >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.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 thewww interface >> or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.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 thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Bharath.K.Chakravarthi Ph:9535629260 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Size of generating data
hi all I'm running simulation for a protein of about 150 amino acids for 100 steps i.e 2 ns in a system of about 35 GB disk space. is there any way to know the approximate size of generating data. -- Bharath.K.Chakravarthi Ph:9535629260 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] simulating the effect of Ph
hello all... i know simulating the effect of temperature and pressure on the protein is there any way to study the effect of Ph on the system -- Bharath.K.Chakravarthi Ph:9535629260 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] is it any serious error
hello all... when ever i run simulation i'm getting this kind of out put saying there is one warning as shown below Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat There are: 4401 OTHER residues There are: 46 PROTEIN residues There are: 0 DNA residues Analysing Protein... Analysing Other... WARNING 1 [file aminoacids.dat, line 1]: T-Coupling group protein has fewer than 10% of the atoms (460 out of 13663) Maybe you want to try Protein and Non-Protein instead? Making dummy/rest group for Acceleration containing 13663 elements Making dummy/rest group for Freeze containing 13663 elements Making dummy/rest group for Energy Mon. containing 13663 elements Making dummy/rest group for VCM containing 13663 elements Number of degrees of freedom in T-Coupling group Protein is 912.90 Number of degrees of freedom in T-Coupling group Other is 26403.10 Making dummy/rest group for User1 containing 13663 elements Making dummy/rest group for User2 containing 13663 elements Making dummy/rest group for XTC containing 13663 elements Making dummy/rest group for Or. Res. Fit containing 13663 elements Making dummy/rest group for QMMM containing 13663 elements T-Coupling has 2 element(s): Protein Other Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1 has 1 element(s): rest User2 has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... Calculating fourier grid dimensions for X Y Z Using a fourier grid of 44x44x44, spacing 0.118 0.118 0.118 writing run input file... There was 1 warning gcq#100: "Proceed, With Fingers Crossed" (TeX) -- Bharath.K.Chakravarthi Ph:9535629260 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] nstfout parameter
hi .. in my *.mdp file one parameter named mstfout is set to 0 can you please tell me the use of this parameter -- Bharath.K.Chakravarthi Ph:9535629260 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] *.xtc file is not getting created by mdrun program :(
Thank you very much for your replay sir... On Wed, Apr 14, 2010 at 5:36 AM, Justin A. Lemkul wrote: > > > Bharath.K. Chakravarthi wrote: > >> sir should i set dat to 0 or what to do >> >> > I clearly stated that you should set nstxtcout > 0 in my first message. > Leaving any output control parameter set to zero means "produce output > every zero steps" or essentially, not at all. > > -Justin > > >> On Wed, Apr 14, 2010 at 5:32 AM, Bharath.K. Chakravarthi < >> bharath.chakravar...@gmail.com <mailto:bharath.chakravar...@gmail.com>> >> wrote: >> >> >> >>On Wed, Apr 14, 2010 at 5:31 AM, Bharath.K. Chakravarthi >>><mailto:bharath.chakravar...@gmail.com>> wrote: >> >>Thank you for your kind replay sir >>sir in my .mdp file there is nstxtout instead of nstxtcout sir >>and it is set to 500 >>is this what u told... >>i have also attached the .mdp file in this mail sir >> >>On Wed, Apr 14, 2010 at 5:18 AM, Justin A. Lemkul >>mailto:jalem...@vt.edu>> wrote: >> >> >> >>Bharath.K. Chakravarthi wrote: >> >>hi there i tried to run MD and i wanted to use *.xtc >>file in vmd to visualize the protein but unfortunately >>there is no such file i given the command like this >>mdrun -nice 0 -v -s input3.tpr -o md_traj.trr -x >>md_traj.xtc -c md_final.gro -e md_ener.edr >>as procedure this should create md_traj.xtc file rite. >> >> >>Provided that you have set nstxtcout > 0 in the .mdp file. >> The default is 0 (no .xtc file). Consult the manual for >>appropriate settings. >> >>-Justin >> >> >>so please can u help me out of this mesh... >> >>-- Bharath.K.Chakravarthi >>Ph:9535629260 >> >> >>-- >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>MILES-IGERT Trainee >>Department of Biochemistry >>Virginia Tech >>Blacksburg, VA >>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> >>-- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> >>http://lists.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 >>gmx-users-requ...@gromacs.org >><mailto:gmx-users-requ...@gromacs.org>. >> >>Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >>-- Bharath.K.Chakravarthi >>Ph:9535629260 >> >> >> >> >>-- Bharath.K.Chakravarthi >>Ph:9535629260 >> >> >> >> >> -- >> Bharath.K.Chakravarthi >> Ph:9535629260 >> > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Bharath.K.Chakravarthi Ph:9535629260 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] *.xtc file is not getting created by mdrun program :(
sir should i set dat to 0 or what to do On Wed, Apr 14, 2010 at 5:32 AM, Bharath.K. Chakravarthi < bharath.chakravar...@gmail.com> wrote: > > > On Wed, Apr 14, 2010 at 5:31 AM, Bharath.K. Chakravarthi < > bharath.chakravar...@gmail.com> wrote: > >> Thank you for your kind replay sir >> sir in my .mdp file there is nstxtout instead of nstxtcout sir and it is >> set to 500 >> is this what u told... >> i have also attached the .mdp file in this mail sir >> >> On Wed, Apr 14, 2010 at 5:18 AM, Justin A. Lemkul wrote: >> >>> >>> >>> Bharath.K. Chakravarthi wrote: >>> >>>> hi there i tried to run MD and i wanted to use *.xtc file in vmd to >>>> visualize the protein but unfortunately there is no such file i given the >>>> command like this >>>> mdrun -nice 0 -v -s input3.tpr -o md_traj.trr -x md_traj.xtc -c >>>> md_final.gro -e md_ener.edr >>>> as procedure this should create md_traj.xtc file rite. >>>> >>> >>> Provided that you have set nstxtcout > 0 in the .mdp file. The default >>> is 0 (no .xtc file). Consult the manual for appropriate settings. >>> >>> -Justin >>> >>> >>> so please can u help me out of this mesh... >>>> >>>> -- >>>> Bharath.K.Chakravarthi >>>> Ph:9535629260 >>>> >>>> >>> -- >>> >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.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 gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> >> >> -- >> Bharath.K.Chakravarthi >> Ph:9535629260 >> > > > > -- > Bharath.K.Chakravarthi > Ph:9535629260 > -- Bharath.K.Chakravarthi Ph:9535629260 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] *.xtc file is not getting created by mdrun program :(
Thank you for your kind replay sir sir in my .mdp file there is nstxtout instead of nstxtcout sir and it is set to 500 is this what u told... i have also attached the .mdp file in this mail sir On Wed, Apr 14, 2010 at 5:18 AM, Justin A. Lemkul wrote: > > > Bharath.K. Chakravarthi wrote: > >> hi there i tried to run MD and i wanted to use *.xtc file in vmd to >> visualize the protein but unfortunately there is no such file i given the >> command like this >> mdrun -nice 0 -v -s input3.tpr -o md_traj.trr -x md_traj.xtc -c >> md_final.gro -e md_ener.edr >> as procedure this should create md_traj.xtc file rite. >> > > Provided that you have set nstxtcout > 0 in the .mdp file. The default is > 0 (no .xtc file). Consult the manual for appropriate settings. > > -Justin > > > so please can u help me out of this mesh... >> >> -- >> Bharath.K.Chakravarthi >> Ph:9535629260 >> >> > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Bharath.K.Chakravarthi Ph:9535629260 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] *.xtc file is not getting created by mdrun program :(
On Wed, Apr 14, 2010 at 5:31 AM, Bharath.K. Chakravarthi < bharath.chakravar...@gmail.com> wrote: > Thank you for your kind replay sir > sir in my .mdp file there is nstxtout instead of nstxtcout sir and it is > set to 500 > is this what u told... > i have also attached the .mdp file in this mail sir > > On Wed, Apr 14, 2010 at 5:18 AM, Justin A. Lemkul wrote: > >> >> >> Bharath.K. Chakravarthi wrote: >> >>> hi there i tried to run MD and i wanted to use *.xtc file in vmd to >>> visualize the protein but unfortunately there is no such file i given the >>> command like this >>> mdrun -nice 0 -v -s input3.tpr -o md_traj.trr -x md_traj.xtc -c >>> md_final.gro -e md_ener.edr >>> as procedure this should create md_traj.xtc file rite. >>> >> >> Provided that you have set nstxtcout > 0 in the .mdp file. The default is >> 0 (no .xtc file). Consult the manual for appropriate settings. >> >> -Justin >> >> >> so please can u help me out of this mesh... >>> >>> -- >>> Bharath.K.Chakravarthi >>> Ph:9535629260 >>> >>> >> -- >> >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > -- > Bharath.K.Chakravarthi > Ph:9535629260 > -- Bharath.K.Chakravarthi Ph:9535629260 md.mdp Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] *.xtc file is not getting created by mdrun program :(
hi there i tried to run MD and i wanted to use *.xtc file in vmd to visualize the protein but unfortunately there is no such file i given the command like this mdrun -nice 0 -v -s input3.tpr -o md_traj.trr -x md_traj.xtc -c md_final.gro -e md_ener.edr as procedure this should create md_traj.xtc file rite. so please can u help me out of this mesh... -- Bharath.K.Chakravarthi Ph:9535629260 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
