Hi Tsjerk, Thanks for helping me. I can run trjconv without nojump. And when I use gmxcheck, it gives the following output:
Warning at frame 5: coordinates for atom 7035 are large (-2.14748e+06) Warning at frame 5: coordinates for atom 7036 are large (-2.14748e+06) Warning at frame 5: coordinates for atom 7036 are large (-2.14748e+06) Warning at frame 5: coordinates for atom 7036 are large (-2.14748e+06) Warning at frame 5: coordinates for atom 7037 are large (-2.14748e+06) Warning at frame 5: coordinates for atom 7037 are large (-2.14748e+06) Doesn't it mean my system is too large? Thank you so much! On Jul 4, 2013, at 3:39 AM, gmx-users-requ...@gromacs.org wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. unwrap trajectory file using -pbc nojump (Yutian Yang) > 2. Re: unwrap trajectory file using -pbc nojump (Tsjerk Wassenaar) > 3. Re: Re: Lennard-Jones potential for protons (Jong Wha Lee) > 4. g_velacc (Ishwor) > 5. Re: g_velacc (David van der Spoel) > 6. Re: g_velacc (Ishwor) > 7. fftw compile error for 4.6.2 (Albert) > 8. Re: Re: g_velacc (David van der Spoel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 3 Jul 2013 19:22:43 +0000 > From: "Yutian Yang" <yyan...@syr.edu> > Subject: [gmx-users] unwrap trajectory file using -pbc nojump > To: "gmx-users@gromacs.org" <gmx-users@gromacs.org> > Message-ID: <11ca0835-fca9-47f9-a4cd-f6ecd6e9a...@syr.edu> > Content-Type: text/plain; charset="us-ascii" > > Dear all, > > I want to remove PBC effects for my system and calculate the diffusion > coefficient. I am using Gromacs 4.5.4. My system is a 15 nm cubic box with > 376 polymer chains each with 28 beads. The simulation time is about 2000 ns. > However, when I use the command > > trjconv_mpi -f all.xtc -s polyeqm.gro -o allnojump.xtc -pbc nojump > > The program stops at around 500 ns. It doesn't get killed, nor proceeds, but > stuck there and I have to manually cease the program. I have tried different > systems with same attributes, all with the same problem. Is it because it is > a large system that makes the program running out of memory? > > Thank you! > > Yutian > > > > > > > > > > > > > > ------------------------------ > > Message: 2 > Date: Wed, 3 Jul 2013 22:03:26 +0200 > From: Tsjerk Wassenaar <tsje...@gmail.com> > Subject: Re: [gmx-users] unwrap trajectory file using -pbc nojump > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <CABzE1ShZzGY509L7Lab-1hD6ZBc=wW_=9Njss_GCA=byuq6...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Yutian Yang, > > I don't think it's because of the size of the system. Can you run trjconv > without -pbc nojump? And did you check the trajectory with gmxcheck? Does > the output file exceed a maximum file size limit? > > Hope it helps, > > Tsjerk > > > On Wed, Jul 3, 2013 at 9:22 PM, Yutian Yang <yyan...@syr.edu> wrote: > >> Dear all, >> >> I want to remove PBC effects for my system and calculate the diffusion >> coefficient. I am using Gromacs 4.5.4. My system is a 15 nm cubic box with >> 376 polymer chains each with 28 beads. The simulation time is about 2000 >> ns. However, when I use the command >> >> trjconv_mpi -f all.xtc -s polyeqm.gro -o allnojump.xtc -pbc nojump >> >> The program stops at around 500 ns. It doesn't get killed, nor proceeds, >> but stuck there and I have to manually cease the program. I have tried >> different systems with same attributes, all with the same problem. Is it >> because it is a large system that makes the program running out of memory? >> >> Thank you! >> >> Yutian >> >> >> >> >> >> >> >> >> >> >> >> -- >> 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/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 >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > > ------------------------------ > > Message: 3 > Date: Thu, 4 Jul 2013 10:58:24 +0900 > From: "Jong Wha Lee" <jongwh...@postech.ac.kr> > Subject: [gmx-users] Re: Re: Lennard-Jones potential for protons > To: <gmx-users@gromacs.org> > Message-ID: <024b01ce7859$f7d97850$e78c68f0$@postech.ac.kr> > Content-Type: text/plain; charset="us-ascii" > > Thank you Mark and Vitaly. > > > > I understand that simulation of protons in the solution phase is unphysical. > Though I haven't mentioned beforehand, I'm actually trying to simulate > noncovalent interaction between a proton and a carbonyl oxygen in the gas > phase. Could you give me any ideas how I may simulate this? > > > > Thank you very much > > > > > > Jong Wha > > > > ------------------------------ > > Message: 4 > Date: Wed, 3 Jul 2013 20:38:01 -0700 (PDT) > From: Ishwor <ishwor.poudya...@gmail.com> > Subject: [gmx-users] g_velacc > To: gmx-users@gromacs.org > Message-ID: <1372909081464-5009541.p...@n6.nabble.com> > Content-Type: text/plain; charset=us-ascii > > Dear all > I have calculated the diffusion coefficient using command g_msd and I want > to calculate diffusion coefficient using command g_velacc. I am confused > with some terms. > 1>I have looked the manual page of g_velacc and i found the statement "the > time interval between data collection points is much shorter than the time > scale of the autocorrelation." What actually does that mean? > 2>I am also confused with the flag -acflen ( I have found that it describes > the number of frames to be taken into consideration.Does that mean I have to > take the points ,to integrate, in such a way that it matches with the time > i have used in g_msd for fitting of Einsteins equation) > 3> what does the flag -nonormalize indicates. Do I need to use it > necessarily? > 4>Is the command "g_analyze -f *.xvg -integrate" sufficient for > integration? > Ishwor > Nepal > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/g-velacc-tp5009541.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > > > ------------------------------ > > Message: 5 > Date: Thu, 04 Jul 2013 07:53:12 +0200 > From: David van der Spoel <sp...@xray.bmc.uu.se> > Subject: Re: [gmx-users] g_velacc > To: gmx-users@gromacs.org > Message-ID: <51d50dc8.8030...@xray.bmc.uu.se> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 2013-07-04 05:38, Ishwor wrote: >> Dear all >> I have calculated the diffusion coefficient using command g_msd and I want >> to calculate diffusion coefficient using command g_velacc. I am confused >> with some terms. >> 1>I have looked the manual page of g_velacc and i found the statement "the >> time interval between data collection points is much shorter than the time >> scale of the autocorrelation." What actually does that mean? >> 2>I am also confused with the flag -acflen ( I have found that it describes >> the number of frames to be taken into consideration.Does that mean I have to >> take the points ,to integrate, in such a way that it matches with the time >> i have used in g_msd for fitting of Einsteins equation) >> 3> what does the flag -nonormalize indicates. Do I need to use it >> necessarily? >> 4>Is the command "g_analyze -f *.xvg -integrate" sufficient for >> integration? >> Ishwor > > Lots of good questions. > Have you actually tried? > > You need to store the Velcoties quite often, maybe every 20 fs > (depending on the system). >> Nepal >> >> >> >> -- >> View this message in context: >> http://gromacs.5086.x6.nabble.com/g-velacc-tp5009541.html >> Sent from the GROMACS Users Forum mailing list archive at Nabble.com. >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > > > ------------------------------ > > Message: 6 > Date: Wed, 3 Jul 2013 23:32:02 -0700 (PDT) > From: Ishwor <ishwor.poudya...@gmail.com> > Subject: [gmx-users] Re: g_velacc > To: gmx-users@gromacs.org > Message-ID: <1372919522806-5009543.p...@n6.nabble.com> > Content-Type: text/plain; charset=us-ascii > > I have really tried to calculate diffusion coefficient using both commands > but i cant find the comparable results. > i have my *.mdp file as > ;PREPROCESSING parameters > tinit = 0 > integrator = md > dt =.002 > nsteps = 100000000 > nstcomm = 1 > > ;OUPUT CONTROL parameters. > nstxout = 500 > nstvout = 500 > nstfout = 500 > nstlog = 500 > nstenergy = 500 > nstxtcout = 500 > energygrps = system > ;NEIGHBOUR SEARCHING parameters. > nstlist = 10 > ns_type = grid > rlist = 1.0 > ;ELECTROSTATIC and VdW parameters. > rcoulomb = 1.0 > rvdw = 1.0 > epsilon-r = 1 > ;BERENDSEN TEMPERATURE COUPLING is on in two groups > Tcoupl = berendsen > tc-grps = system > tau_t = 0.1 > ref_t = 303 > > ;PRESSURE COUPLING is on > Pcoupl = no > gen_vel = no; > ;BONDS parameters > constraints = all-bonds > constraint-algorithm = shake > unconstrained-start = yes > pbc = xyz > i have calculated the diffusion coefficient using Einsteins law and found > 2.40*10^-5 cm^2/s. I have used 2 ns time to fit the curve. > To calculate the diffusion coefficient using g_velacc i used the command > g_velacc -f nvt.trr -s nvt.tpr -n index.ndx -o vac.xvg -nonormalize -acflen > 2001 -mol > and integrate using g_analyze -f vac.xvg -integrate > but i found the result > Calculating the integral using the trapezium rule > Integral 1 0.11915 +/- 0.00000 > std. dev. relative deviation of > standard --------- cumulants from those of > set average deviation sqrt(n-1) a Gaussian distribition > cum. 3 cum. 4 > SS1 1.262569e-04 5.975760e-03 1.336220e-04 27.976 664.233 > > I guess the required integral value is 0.11915 and to find diffusion > coefficient i divide the result by 3 but get the result not matching with > the one found using g_msd. i guess the value 0.11915 is in unit nm^2/ps. > I dont know whether i am in the correct path or there is some problems with > my doings. > i am waiting for the suggestions > Thanks > > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/g-velacc-tp5009541p5009543.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > > > ------------------------------ > > Message: 7 > Date: Thu, 04 Jul 2013 09:09:32 +0200 > From: Albert <mailmd2...@gmail.com> > Subject: [gmx-users] fftw compile error for 4.6.2 > To: gromacs maillist <gmx-users@gromacs.org> > Message-ID: <51d51fac.3040...@gmail.com> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Hello: > > I am trying to compile Gromacs-4.6.2 for a GPU cluster with following > command: > > > CC=icc FC=ifort F77=ifort CXX=icpc > CMAKE_PREFIX_PATH=/export/intel/cmkl/include/fftw:/export/mpi/mvapich2.amd/1.4 > > cmake .. -DGMX_MPI=ON > -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs -DGMX_GPU=ON > -DBUILD_SHARED_LIBS=OFF -DCUDA_TOOLKIT_ROOT_DIR=/export/cuda5.0 > -DFFTWF_LIBRARY= /export/fftw-3.3.3 > > but it always claimed errors for fftw: > > > > -- Found PkgConfig: /usr/bin/pkg-config (found version "0.21") > -- checking for module 'fftw3f' > -- package 'fftw3f' not found > -- pkg-config could not detect fftw3f, trying generic detection > -- Looking for fftwf_plan_r2r_1d in /export/fftw-3.3.3/lib > WARNING: Target "cmTryCompileExec1612346837" requests linking to > directory "/export/fftw-3.3.3/lib". Targets may link only to > libraries. CMake is dropping the item. > -- Looking for fftwf_plan_r2r_1d in /export/fftw-3.3.3/lib - not found > CMake Error at cmake/FindFFTW.cmake:97 (message): > Could not find fftwf_plan_r2r_1d in /export/fftw-3.3.3/lib, take a > look at > the error message in > /home/albert/install/gromacs-4.6.2/build/CMakeFiles/CMakeError.log to > find > out what went wrong. If you are using a static lib (.a) make sure > you have > specified all dependencies of fftw3f in FFTWF_LIBRARY by hand (e.g. > -DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') ! > Call Stack (most recent call first): > CMakeLists.txt:943 (find_package) > > > -- Configuring incomplete, errors occurred! > > > I compiled fftw with options: > > ./configure CC=icc CXX=icpc F77=ifort FC=ifort > --prefix=/home/albert/install/fftw-3.3.3 --enable-float --with-pic > --enable-single --enable-static --enable-mpi > > and I don't find so called "libfftw3f.so" in the fftw installation > directory. > > does anybody have any advices? > > THX > > Albert > > > > ------------------------------ > > Message: 8 > Date: Thu, 04 Jul 2013 09:39:23 +0200 > From: David van der Spoel <sp...@xray.bmc.uu.se> > Subject: Re: [gmx-users] Re: g_velacc > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <51d526ab.20...@xray.bmc.uu.se> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 2013-07-04 08:32, Ishwor wrote: >> I have really tried to calculate diffusion coefficient using both commands >> but i cant find the comparable results. >> i have my *.mdp file as >> ;PREPROCESSING parameters >> tinit = 0 >> integrator = md >> dt =.002 >> nsteps = 100000000 >> nstcomm = 1 >> >> ;OUPUT CONTROL parameters. >> nstxout = 500 >> nstvout = 500 >> nstfout = 500 >> nstlog = 500 >> nstenergy = 500 >> nstxtcout = 500 >> energygrps = system >> ;NEIGHBOUR SEARCHING parameters. >> nstlist = 10 >> ns_type = grid >> rlist = 1.0 >> ;ELECTROSTATIC and VdW parameters. >> rcoulomb = 1.0 >> rvdw = 1.0 >> epsilon-r = 1 >> ;BERENDSEN TEMPERATURE COUPLING is on in two groups >> Tcoupl = berendsen >> tc-grps = system >> tau_t = 0.1 >> ref_t = 303 >> >> ;PRESSURE COUPLING is on >> Pcoupl = no >> gen_vel = no; >> ;BONDS parameters >> constraints = all-bonds >> constraint-algorithm = shake >> unconstrained-start = yes >> pbc = xyz >> i have calculated the diffusion coefficient using Einsteins law and found >> 2.40*10^-5 cm^2/s. I have used 2 ns time to fit the curve. >> To calculate the diffusion coefficient using g_velacc i used the command >> g_velacc -f nvt.trr -s nvt.tpr -n index.ndx -o vac.xvg -nonormalize -acflen >> 2001 -mol >> and integrate using g_analyze -f vac.xvg -integrate >> but i found the result >> Calculating the integral using the trapezium rule >> Integral 1 0.11915 +/- 0.00000 >> std. dev. relative deviation of >> standard --------- cumulants from those of >> set average deviation sqrt(n-1) a Gaussian distribition >> cum. 3 cum. 4 >> SS1 1.262569e-04 5.975760e-03 1.336220e-04 27.976 664.233 >> >> I guess the required integral value is 0.11915 and to find diffusion >> coefficient i divide the result by 3 but get the result not matching with >> the one found using g_msd. i guess the value 0.11915 is in unit nm^2/ps. >> I dont know whether i am in the correct path or there is some problems with >> my doings. >> i am waiting for the suggestions > > nstvout = 10 > >> Thanks >> >> >> >> >> -- >> View this message in context: >> http://gromacs.5086.x6.nabble.com/g-velacc-tp5009541p5009543.html >> Sent from the GROMACS Users Forum mailing list archive at Nabble.com. >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > > > ------------------------------ > > -- > 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/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 111, Issue 14 > ****************************************** > -- 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/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
