[gmx-users] parameters for output control
Dear Mark, Thank you very much from your help. Best Regards Sara - Original Message - From: Mark Abraham To: Discussion list for GROMACS users Cc: Sent: Tuesday, August 21, 2012 9:45 AM Subject: Re: [gmx-users] parameters for output control On 21/08/2012 2:55 PM, mohammad agha wrote: > Dear Justin, > > Thank you very much from your response. Yes, I said bad!!! > My question is: For example, when I select -b 8 and Gromacs reads as (in > the last step of reading from output file): Reading frame 13000 time > 860040.000 , does it perform the computation untill time= 860040 ps or not? > or does Gromacs perform the computations untill end of simulation (90 ps) > and only doesn't printe in the command line? You asked for everything after time 8, and that's what you got. If you really want to be sure, use trjconv to make the subset of the trajectory, verify its content with gmxcheck or gmxdump, and use g_rdf on that. And then observe you get the same result as you already have. Mark > > Best Reagrds > Sara > - Original Message - > From: Justin Lemkul > To: mohammad agha ; Discussion list for GROMACS users > > Cc: > Sent: Monday, August 20, 2012 10:45 AM > Subject: Re: [gmx-users] parameters for output control > > > > On 8/20/12 1:15 PM, mohammad agha wrote: >> Dear Gromacs Users, >> >> I have one problem about the way of computation in the Gromacs with frame >> and time. (I work with MARTINI CG) >> I have one md.mdp file that the parameters of output control in it is as >> follows: >> nsteps = 3000 >> dt = 0.030 >> ; Output control >> nstxout = 2000 >> nstvout = 2000 >> nstenergy = 2000 >> nstlog = 2000 >> nstxtcout = 2000 >> xtc_precision = 1000 >> Consequently, total time of my system is 90 ps.When I want to obtaine >> some information about my system for example RDF by g_rdf command, >> computation of Gromacs perfome as follows: >> Reading frame 200 time 12000.000 >> .300 >> .400 >> .500 >> .600 >> .700 >> ... >> ... >> ... >> Reading frame 2000 time 12.000 >> .3000 >> .4000 >> .5000 >> .6000 >> .7000 >> ... >> ... >> ... >> Last frame 15000 time 90.000 >> It means that until frame 2000 reading is 100 to 100 in frames and from 2000 >> to end, it is 1000 to 1000. > I don't understand this assertion. You have frames every 60 ps, as expected. > Console output is buffered so that the programs are not wasting time > continually updating the frame number and time value. > >> Also, I did with this parameters: >> ; Output control >> nstxout = 200 >> nstvout = 200 >> nstenergy = 100 >> nstlog = 200 >> nstxtcout = 200 >> xtc_precision = 100 >> but the result of reading the frames was the same previous. >> I want to Gromacs read frames 100 to 100 not 1000 to 1000, because I find >> problem when I use -b in g_rdf command. for eaxample, with -b 8, reading >> is only until 860040 ps, Reading frame 13000 time 860040.000 ,not until end >> of simulation (90). > This sounds like the same issue above. The console output may be incomplete. > It's merely a convenience to have an estimate of how long the calculation is > taking. > >> Also, I want to have smaller systems with smaller volume by convert 2000 to >> 1 for parameters for output control but I want reading from frame for >> computation of properties become 100 frames to 100 frames or 10 frames to 10 >> frames. >> > I also don't understand this statement so I can't offer anything to > particularly useful to help. > > -Justin > > -- > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 * Only plain text messages are allowed! * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] parameters for output control
On 21/08/2012 2:55 PM, mohammad agha wrote: Dear Justin, Thank you very much from your response. Yes, I said bad!!! My question is: For example, when I select -b 8 and Gromacs reads as (in the last step of reading from output file): Reading frame 13000 time 860040.000 , does it perform the computation untill time= 860040 ps or not? or does Gromacs perform the computations untill end of simulation (90 ps) and only doesn't printe in the command line? You asked for everything after time 8, and that's what you got. If you really want to be sure, use trjconv to make the subset of the trajectory, verify its content with gmxcheck or gmxdump, and use g_rdf on that. And then observe you get the same result as you already have. Mark Best Reagrds Sara - Original Message - From: Justin Lemkul To: mohammad agha ; Discussion list for GROMACS users Cc: Sent: Monday, August 20, 2012 10:45 AM Subject: Re: [gmx-users] parameters for output control On 8/20/12 1:15 PM, mohammad agha wrote: Dear Gromacs Users, I have one problem about the way of computation in the Gromacs with frame and time. (I work with MARTINI CG) I have one md.mdp file that the parameters of output control in it is as follows: nsteps = 3000 dt = 0.030 ; Output control nstxout = 2000 nstvout = 2000 nstenergy = 2000 nstlog = 2000 nstxtcout = 2000 xtc_precision = 1000 Consequently, total time of my system is 90 ps.When I want to obtaine some information about my system for example RDF by g_rdf command, computation of Gromacs perfome as follows: Reading frame 200 time 12000.000 .300 .400 .500 .600 .700 ... ... ... Reading frame 2000 time 12.000 .3000 .4000 .5000 .6000 .7000 ... ... ... Last frame 15000 time 90.000 It means that until frame 2000 reading is 100 to 100 in frames and from 2000 to end, it is 1000 to 1000. I don't understand this assertion. You have frames every 60 ps, as expected. Console output is buffered so that the programs are not wasting time continually updating the frame number and time value. Also, I did with this parameters: ; Output control nstxout = 200 nstvout = 200 nstenergy = 100 nstlog = 200 nstxtcout = 200 xtc_precision = 100 but the result of reading the frames was the same previous. I want to Gromacs read frames 100 to 100 not 1000 to 1000, because I find problem when I use -b in g_rdf command. for eaxample, with -b 8, reading is only until 860040 ps, Reading frame 13000 time 860040.000 ,not until end of simulation (90). This sounds like the same issue above. The console output may be incomplete. It's merely a convenience to have an estimate of how long the calculation is taking. Also, I want to have smaller systems with smaller volume by convert 2000 to 1 for parameters for output control but I want reading from frame for computation of properties become 100 frames to 100 frames or 10 frames to 10 frames. I also don't understand this statement so I can't offer anything to particularly useful to help. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] parameters for output control
Dear Justin, Thank you very much from your response. Yes, I said bad!!! My question is: For example, when I select -b 8 and Gromacs reads as (in the last step of reading from output file): Reading frame 13000 time 860040.000 , does it perform the computation untill time= 860040 ps or not? or does Gromacs perform the computations untill end of simulation (90 ps) and only doesn't printe in the command line? Best Reagrds Sara - Original Message - From: Justin Lemkul To: mohammad agha ; Discussion list for GROMACS users Cc: Sent: Monday, August 20, 2012 10:45 AM Subject: Re: [gmx-users] parameters for output control On 8/20/12 1:15 PM, mohammad agha wrote: > Dear Gromacs Users, > > I have one problem about the way of computation in the Gromacs with frame and > time. (I work with MARTINI CG) > I have one md.mdp file that the parameters of output control in it is as > follows: > nsteps = 3000 > dt = 0.030 > ; Output control > nstxout = 2000 > nstvout = 2000 > nstenergy = 2000 > nstlog = 2000 > nstxtcout = 2000 > xtc_precision = 1000 > Consequently, total time of my system is 90 ps.When I want to obtaine > some information about my system for example RDF by g_rdf command, > computation of Gromacs perfome as follows: > Reading frame 200 time 12000.000 > .300 > .400 > .500 > .600 > .700 > ... > ... > ... > Reading frame 2000 time 12.000 > .3000 > .4000 > .5000 > .6000 > .7000 > ... > ... > ... > Last frame 15000 time 90.000 > It means that until frame 2000 reading is 100 to 100 in frames and from 2000 > to end, it is 1000 to 1000. I don't understand this assertion. You have frames every 60 ps, as expected. Console output is buffered so that the programs are not wasting time continually updating the frame number and time value. > Also, I did with this parameters: > ; Output control > nstxout = 200 > nstvout = 200 > nstenergy = 100 > nstlog = 200 > nstxtcout = 200 > xtc_precision = 100 > but the result of reading the frames was the same previous. > I want to Gromacs read frames 100 to 100 not 1000 to 1000, because I find > problem when I use -b in g_rdf command. for eaxample, with -b 8, reading > is only until 860040 ps, Reading frame 13000 time 860040.000 ,not until end > of simulation (90). This sounds like the same issue above. The console output may be incomplete. It's merely a convenience to have an estimate of how long the calculation is taking. > Also, I want to have smaller systems with smaller volume by convert 2000 to > 1 for parameters for output control but I want reading from frame for > computation of properties become 100 frames to 100 frames or 10 frames to 10 > frames. > I also don't understand this statement so I can't offer anything to particularly useful to help. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] parameters for output control
On 8/20/12 1:15 PM, mohammad agha wrote: Dear Gromacs Users, I have one problem about the way of computation in the Gromacs with frame and time. (I work with MARTINI CG) I have one md.mdp file that the parameters of output control in it is as follows: nsteps = 3000 dt = 0.030 ; Output control nstxout = 2000 nstvout = 2000 nstenergy = 2000 nstlog = 2000 nstxtcout = 2000 xtc_precision = 1000 Consequently, total time of my system is 90 ps.When I want to obtaine some information about my system for example RDF by g_rdf command, computation of Gromacs perfome as follows: Reading frame 200 time 12000.000 .300 .400 .500 .600 .700 ... ... ... Reading frame 2000 time 12.000 .3000 .4000 .5000 .6000 .7000 ... ... ... Last frame 15000 time 90.000 It means that until frame 2000 reading is 100 to 100 in frames and from 2000 to end, it is 1000 to 1000. I don't understand this assertion. You have frames every 60 ps, as expected. Console output is buffered so that the programs are not wasting time continually updating the frame number and time value. Also, I did with this parameters: ; Output control nstxout = 200 nstvout = 200 nstenergy = 100 nstlog = 200 nstxtcout = 200 xtc_precision = 100 but the result of reading the frames was the same previous. I want to Gromacs read frames 100 to 100 not 1000 to 1000, because I find problem when I use -b in g_rdf command. for eaxample, with -b 8, reading is only until 860040 ps, Reading frame 13000 time 860040.000 ,not until end of simulation (90). This sounds like the same issue above. The console output may be incomplete. It's merely a convenience to have an estimate of how long the calculation is taking. Also, I want to have smaller systems with smaller volume by convert 2000 to 1 for parameters for output control but I want reading from frame for computation of properties become 100 frames to 100 frames or 10 frames to 10 frames. I also don't understand this statement so I can't offer anything to particularly useful to help. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] parameters for output control
Dear Gromacs Users, I have one problem about the way of computation in the Gromacs with frame and time. (I work with MARTINI CG) I have one md.mdp file that the parameters of output control in it is as follows: nsteps = 3000 dt = 0.030 ; Output control nstxout = 2000 nstvout = 2000 nstenergy = 2000 nstlog = 2000 nstxtcout = 2000 xtc_precision = 1000 Consequently, total time of my system is 90 ps.When I want to obtaine some information about my system for example RDF by g_rdf command, computation of Gromacs perfome as follows: Reading frame 200 time 12000.000 .300 .400 .500 .600 .700 ... ... ... Reading frame 2000 time 12.000 .3000 .4000 .5000 .6000 .7000 ... ... ... Last frame 15000 time 90.000 It means that until frame 2000 reading is 100 to 100 in frames and from 2000 to end, it is 1000 to 1000. Also, I did with this parameters: ; Output control nstxout = 200 nstvout = 200 nstenergy = 100 nstlog = 200 nstxtcout = 200 xtc_precision = 100 but the result of reading the frames was the same previous. I want to Gromacs read frames 100 to 100 not 1000 to 1000, because I find problem when I use -b in g_rdf command. for eaxample, with -b 8, reading is only until 860040 ps, Reading frame 13000 time 860040.000 ,not until end of simulation (90). Also, I want to have smaller systems with smaller volume by convert 2000 to 1 for parameters for output control but I want reading from frame for computation of properties become 100 frames to 100 frames or 10 frames to 10 frames. May I ask you to help me, Please? Thank you very much in advance. Best Regards Sara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
