[gmx-users] How to convert a cpt file to an old version of gromacs
Dear Gromacs users, Can anyone please help me how can I convert a cpt file from a new to an older Gromacs version? Thanks -- gmx-users mailing listgmx-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
Re: [gmx-users] how to convert a file
Dear Mark, Thank you, I did it already :) I tried to make a nick name because the actual contains personal informations but always google knows every thing ;) Some additional fun also with using Gromacs when there is a luck of concentration ;) On 4 July 2013 22:44, Mark Abraham wrote: > Google knows them better than I :-) > > Mark > > On Thu, Jul 4, 2013 at 2:05 PM, Souilem Safa > wrote: > > Dear Mark , > > Thank you for your quick reply. > > Could you please provide me a tutorial link example ? I will be grateful. > > Thank you very much > > > > > > On 4 July 2013 21:00, Mark Abraham wrote: > > > >> You can't convert a .tpr file's version in either direction. We try to > >> make the .tpr format backwards compatible, inasmuch as an old .tpr > >> should generally still work with new code. > >> > >> For learning about the process of building one, check out some > >> tutorial material online. > >> > >> Mark > >> > >> On Thu, Jul 4, 2013 at 1:43 PM, natalie gara > >> wrote: > >> > Dear Gromacs users, > >> > > >> > I want to convert a tpr file from different version of Gromacs, I have > >> > looked in the archive, I found that I have to use regenerate but I > didn't > >> > understand exactly if it is a command or a special program that I > have to > >> > use. Could you please inform me about since I a new gromacs user? > >> > Thank you very muchh > >> > -- > >> > gmx-users mailing listgmx-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 > >> -- > >> gmx-users mailing listgmx-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 > >> > > -- > > gmx-users mailing listgmx-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 > -- > gmx-users mailing listgmx-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 > -- gmx-users mailing listgmx-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
Re: [gmx-users] how to convert a file
Dear Mark , Thank you for your quick reply. Could you please provide me a tutorial link example ? I will be grateful. Thank you very much On 4 July 2013 21:00, Mark Abraham wrote: > You can't convert a .tpr file's version in either direction. We try to > make the .tpr format backwards compatible, inasmuch as an old .tpr > should generally still work with new code. > > For learning about the process of building one, check out some > tutorial material online. > > Mark > > On Thu, Jul 4, 2013 at 1:43 PM, natalie gara > wrote: > > Dear Gromacs users, > > > > I want to convert a tpr file from different version of Gromacs, I have > > looked in the archive, I found that I have to use regenerate but I didn't > > understand exactly if it is a command or a special program that I have to > > use. Could you please inform me about since I a new gromacs user? > > Thank you very muchh > > -- > > gmx-users mailing listgmx-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 > -- > gmx-users mailing listgmx-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 > -- gmx-users mailing listgmx-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
[gmx-users] equilibration error
Dear Gromacs users, I tried to do the simulation of a single molecule in cyclohexane, I'm using gromos 53a6 force field for both molecules. i did all the minimization steps. After npt, I runned for 25 000 000 steps. just after around 100 000 steps, the system stops and i got this fatal error: Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated Then I back again to npt step to equilibrate for longer time as the error message said to me, I equilibrate for 500 000 steps instead of 25 steps setted in the mdp file, but again I got the same error. What should I do to overcome this problem? Thank you very much -- gmx-users mailing listgmx-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
[gmx-users] A charge group moved too far between two domain decomposition steps
Dear Gromacs users, I tried to do the simulation of a single molecule in cyclohexane, I'm using gromos 53a6 force field for both molecules. i did all the minimization steps. After npt, I runned for 25 000 000 steps. just after around 100 000 steps, the system stops and i got this fatal error: Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated Then I back again to npt step to equilibrate for longer time as the error message said to me, I equilibrate for 500 000 steps instead of 25 steps setted in the mdp file, but again I got the same error. What should I do to overcome this problem? Thank you very much -- gmx-users mailing listgmx-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
Re: [gmx-users] Error in grompp minimization
Dear Justin, thank you for your reply. Yes, you are right , I have corrected it already and now it works well. Cheers, Safa On 11 June 2013 09:53, Justin Lemkul wrote: > > > On 6/10/13 8:51 PM, Souilem Safa wrote: > >> Dear gromacs users, >> >> I'm trying to simulate a single molecule in cyclohexane. >> I made a box of my molecule using editconf command and next I solvate with >> cyclohexane using genbox command : >> genbox -cp newbox_DRG.gro -cs chx.gro -p chx_DRG.top -o chx_DRG.gro >> >> I did next a position restraint in the topolgy file and I tried to >> minimize, i got this fatal error: >> Fatal error: >> No such moleculetype CHX >> >> What could be the origin of this error. >> > > You probably forgot to #include the topology that introduces CHX as a > valid [moleculetype]. > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing listgmx-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
[gmx-users] Error in grompp minimization
Dear gromacs users, I'm trying to simulate a single molecule in cyclohexane. I made a box of my molecule using editconf command and next I solvate with cyclohexane using genbox command : genbox -cp newbox_DRG.gro -cs chx.gro -p chx_DRG.top -o chx_DRG.gro I did next a position restraint in the topolgy file and I tried to minimize, i got this fatal error: Fatal error: No such moleculetype CHX What could be the origin of this error. Thanks :) -- gmx-users mailing listgmx-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
Re: [gmx-users] building OLPSAA force field
Dear Mark, thank you for your answer, I'm doing it right now. Cheers, Safa On 10 June 2013 14:02, Mark Abraham wrote: > Hi, > > Please do search for GROMACS tutorial material, which will help you get > started with the basic concepts. > > Cheers, > > Mark > > > On Mon, Jun 10, 2013 at 6:34 AM, Souilem Safa >wrote: > > > Dear Gromacs users, > > I'm still relatively new to molecular modelling. > > I want to build a OPLSAA toplogy file of my molecule. I have only the pdb > > file of my molecule. > > Can any one help me what detailed steps should I follow to get that > topolgy > > file. > > Many thanks > > -- > > gmx-users mailing listgmx-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 > > > -- > gmx-users mailing listgmx-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 > -- gmx-users mailing listgmx-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
[gmx-users] building OLPSAA force field
Dear Gromacs users, I'm still relatively new to molecular modelling. I want to build a OPLSAA toplogy file of my molecule. I have only the pdb file of my molecule. Can any one help me what detailed steps should I follow to get that topolgy file. Many thanks -- gmx-users mailing listgmx-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
Re: [gmx-users] changing the version of file
Dear Justin, Thank you very much for your quick response Cheers, Safa On 8 June 2013 12:07, Justin Lemkul wrote: > > > On 6/7/13 11:05 PM, Souilem Safa wrote: > >> Dear Gromacs users, >> >> I'm aiming to extract a frame file from a reduced trajectory, i did the >> simulation on gromacs version 4.6.1 and I would like to do my analysis in >> gromacs 4.5.6 for availability reasons. >> When I entered my command , I got this error : >> reading tpx file (md.tpr) version 83 with version 73 program >> >> Can any one help me how shoud I do to overcome this problem? >> > > Re-generate the .tpr file with the desired version, in this case, 4.5.6. > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing listgmx-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
[gmx-users] changing the version of file
Dear Gromacs users, I'm aiming to extract a frame file from a reduced trajectory, i did the simulation on gromacs version 4.6.1 and I would like to do my analysis in gromacs 4.5.6 for availability reasons. When I entered my command , I got this error : reading tpx file (md.tpr) version 83 with version 73 program Can any one help me how shoud I do to overcome this problem? Many thanks Safa -- gmx-users mailing listgmx-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
Re: [gmx-users] assembling trajectory files
Dear Justin, Thank you very much for your quick reply, that is helpful to me On 4 June 2013 10:05, Justin Lemkul wrote: > > > On 6/3/13 8:54 PM, Souilem Safa wrote: > >> Dear Gromacs users, >> I have simulated my system for two separately 10 ns with continuation >> option in order to continue the first 10 ns simulation. >> In order to do some analysis , I'm aiming to assemble both trajectory and >> tpr files. >> I would be very grateful if someone could help me in this issue. >> >> > trjcat concatenates trajectories. There is no need to concatenate .tpr > files; there are no time-dependent quantities in them so it doesn't make > sense to do so. > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing listgmx-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
[gmx-users] assembling trajectory files
Dear Gromacs users, I have simulated my system for two separately 10 ns with continuation option in order to continue the first 10 ns simulation. In order to do some analysis , I'm aiming to assemble both trajectory and tpr files. I would be very grateful if someone could help me in this issue. -- gmx-users mailing listgmx-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
[gmx-users] simulation single molecule in water
Dear gromacs users, I'm simulating a single molecule in spc water. I'm using a cubic water box which has 3.4 nm size. I got the toplogy of my molecule via PRODRG. After running minimization, NVT , NPT and MD for 10 ns , I checked the density of water ,it was less than the real value (1000 kg m\S-3\N) ,actually I got around 950. I have checked my mdp file in the NPT step and I was wondering about tau_p that I should use. First I used 2.0 ps with Parrinello-Rahman coupling. After checking in gromacs archive, I found it is better to use 0.5 ps, I have changed tau-p ,but I still have density value less than 1000. Details of my mdp file are below : Run parameters integrator= md; leap-frog integrator nsteps= 500; 2 * 500 = 1 ps, 1 ns dt= 0.002; 2 fs ; Output control nstxout= 1000; save coordinates every 2 ps nstvout= 1000; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 2 ps nstenergy= 1000; save energies every 2 ps nstlog= 1000; update log file every 2 ps ; Bond parameters continuation= yes; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= system; two coupling groups - more accurate tau_t= 0.1; time constant, in ps ref_t= 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= isotropic; uniform scaling of box vectors tau_p= 0.50; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= no; Velocity generation is off What should be the origin of this density difference? looking forward to your advise -- gmx-users mailing listgmx-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
Re: [gmx-users] installation Gromacs-Fedora18
many thanks to you all, I did installation as root it works well I like gromacs users discussion. It is very useful :) On 3 May 2013 19:10, Francesco wrote: > this is what I do to install gromacs 4.5.5 on fedora 18 > > fftw libraries > > cd fftw-3.3.3_folder > ./configure --enable-threads --enable-shared --enable-float > --prefix=/usr/local/fftw > make > make install > make clean > > in this way I install single precision (--enable-float) fftw libraries > in /usr/local/fftw (you can put it where you want) > be sure to enable shared because gromacs seems need it > > if you want double precision remove --enable-float > > gromacs 4.5.5 > > cd to folder > ./configure CPPFLAGS="-I/usr/local/fftw/include" > LDFLAGS="-L/usr/localfftw/lib" --with-fft=fftw3 > make > make install > make clean > > --disable-float for double precision and --enable-mpi if you need mpi > > remember that fftw and gromacs must have the same precision. > > hope this helps you > > cheers > > Francesco > > On Fri, 3 May 2013, at 09:39 AM, Souilem Safa wrote: > > Dear Gromacs users, > > I m aiming to install gromacs 4.5.5 package in in linux Fedora 18. I have > > updated the needed compilers and downloaded the fftw-3.3.2.tar.gz and > > gromacs4.5.5.tar.gz > > > > I have followed these commands to install: > > $ tar -zxvf fftw-3.3.2/ > > $ cd fftw-3.3.2/ > > $ ./configure --prefix /home/safa/programs/fftw-3.3.2 --enable-threads > > --enable-sse2 --enable-shared > > $ make > > $ make install > > $ cd > > $ tar zxvf gromacs-4.5.5.tar.gz > > $ cd gromac-4.5.5/ > > $../configure --prefix /home/safa/programs/gromacs-4.5.5 > > LDFLAGS="-L/home/safa/fftw-3.3.2/lib" > > CPPFLAGS="-I/home/safa/programs/fftw-3.3.2/include" --disable-float > > When I wrote the last command I got this error. > > checking build system type... x86_64-unknown-linux-gnu > > checking host system type... x86_64-unknown-linux-gnu > > checking for a BSD-compatible install... /usr/bin/install -c > > checking whether build environment is sane... yes > > checking for a thread-safe mkdir -p... /usr/bin/mkdir -p > > checking for gawk... gawk > > checking whether make sets $(MAKE)... yes > > checking how to create a ustar tar archive... gnutar > > checking for cc... cc > > checking for C compiler default output file name... a.out > > checking whether the C compiler works... yes > > checking whether we are cross compiling... no > > checking for suffix of executables... > > checking for suffix of object files... o > > checking whether we are using the GNU C compiler... yes > > checking whether cc accepts -g... yes > > checking for cc option to accept ISO C89... none needed > > checking for style of include used by make... GNU > > checking dependency style of cc... gcc3 > > checking dependency style of cc... gcc3 > > checking how to run the C preprocessor... cc -E > > checking for grep that handles long lines and -e... /usr/bin/grep > > checking for egrep... /usr/bin/grep -E > > checking whether ln -s works... yes > > checking whether cc accepts -O3... yes > > checking whether cc accepts -msse2... yes > > checking whether cc accepts -funroll-all-loops... yes > > checking whether cc accepts -std=gnu99... yes > > checking whether cc accepts -fexcess-precision=fast... yes > > checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions > > -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 > > -fexcess-precision=fast... yes > > checking for ANSI C header files... yes > > checking for sys/types.h... yes > > checking for sys/stat.h... yes > > checking for stdlib.h... yes > > checking for string.h... yes > > checking for memory.h... yes > > checking for strings.h... yes > > checking for inttypes.h... yes > > checking for stdint.h... yes > > checking for unistd.h... yes > > checking for unistd.h... (cached) yes > > checking sys/time.h usability... yes > > checking sys/time.h presence... yes > > checking for sys/time.h... yes > > checking sched.h usability... yes > > checking sched.h presence... yes > > checking for sched.h... yes > > checking for sysconf... yes > > checking for the pthreads library -lpthreads... no > > checking whether pthreads work without any flags... no > > checking whether pthreads work with -Kthread... no > > checking whether pthreads work with -kthread... no > > checking for the pthreads library -llthread... no > > checking whether pthreads work with -pthread...
[gmx-users] installation Gromacs-Fedora18
Dear Gromacs users, I m aiming to install gromacs 4.5.5 package in in linux Fedora 18. I have updated the needed compilers and downloaded the fftw-3.3.2.tar.gz and gromacs4.5.5.tar.gz I have followed these commands to install: $ tar -zxvf fftw-3.3.2/ $ cd fftw-3.3.2/ $ ./configure --prefix /home/safa/programs/fftw-3.3.2 --enable-threads --enable-sse2 --enable-shared $ make $ make install $ cd $ tar zxvf gromacs-4.5.5.tar.gz $ cd gromac-4.5.5/ $../configure --prefix /home/safa/programs/gromacs-4.5.5 LDFLAGS="-L/home/safa/fftw-3.3.2/lib" CPPFLAGS="-I/home/safa/programs/fftw-3.3.2/include" --disable-float When I wrote the last command I got this error. checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking whether ln -s works... yes checking whether cc accepts -O3... yes checking whether cc accepts -msse2... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -std=gnu99... yes checking whether cc accepts -fexcess-precision=fast... yes checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast... yes checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sysconf... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking if atomic operations are supported... yes checking if pthread_setaffinity_np is available... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /usr/bin/sed checking for ld used by cc ... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from cc object... ok checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if cc supports -fno-rtti -fno-exceptions... no checking for cc option to produce PIC... -fPIC checking if cc PIC flag -fPIC works... yes checking if cc static flag -static works... no checking if cc supports -c -o file.o... yes checking whether the cc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library
Re: [gmx-users] vacum simulation
many thanks to all of you. I have decreased the time step. Simulation has finished in right conditions On 3 May 2013 03:06, Dr. Vitaly Chaban wrote: > LINCS doesn't like your system... or your system doesn't like LINCS... > > You can decrease the time-step as the simplest action. > > Dr. Vitaly Chaban > > > > > > > > > On Thu, May 2, 2013 at 2:40 PM, Souilem Safa > wrote: > > > Dear Gromacs users , > > I did the simulation of a single molecule in vacum. I have choosed 10 ns > > which corresponds to 500 steps. I was checking the .log file > > frequently. > > I have noticed that the number of steps from 1938900 didn't increases. > > When I open a new tab with the top option, I see mdrun still existing. > > I have attached here the .log file and also some warnings that I saw when > > steps stop at 1938900 > > > > Step 1938969, time 3877.94 (ps) LINCS WARNING > > relative constraint deviation after LINCS: > > rms 12871303501.643789, max 33207281664.00 (between atoms 3 and 6) > > bonds that rotated more than 30 degrees: > > atom 1 atom 2 angle previous, current, constraint length > > 46 47 98.80.1406 3889.8669 0.1000 > > 45 46 79.4 10193.8799 10564.2393 0.1440 > > 43 44 79.60.1033 631.2256 0.1000 > > 42 45 80.1 10193.9062 11014.6123 0.1520 > > 42 43 93.50.1851 4970.4243 0.1440 > > 40 41 76.50.1009 184.9659 0.1000 > > 39 42 90.40.1819 5231.5186 0.1520 > > 39 40 100.00.1502 624.0559 0.1440 > > 37 38 97.10.1001 592.4050 0.1000 > > 36 37 81.40.1469 828.7896 0.1430 > > 35 39 88.60.1742 8071.4395 0.1520 > > 35 36 94.70.1861 8093.3452 0.1530 > > 35 34 92.9 8046.3804 17904.5762 0.1440 > > 33 45 78.0 26093.2402 332765.5000 0.1520 > > 33 34 94.6 26065.5371 330302.5625 0.1440 > > 29 30 74.4 190965.5938 1213272. 0.1360 > > 27 28 91.2 85465.0547 294693.5000 0.1430 > > 25 27 85.7 126649.9141 1143663.7500 0.1360 > > 25 26 107.7 116051.3750 805165.8125 0.1230 > > 24 29 102.8 1939418.3750 1702562.5000 0.1390 > > 24 25 101.0 1963544.3750 1402288.3750 0.1390 > > 22 23 97.9 345568.0625 1364901. 0.1530 > > 31 21 109.7 1948370.1250 7003795.5000 0.1390 > > 21 22 101.2 2108572.2500 6662917.5000 0.1390 > > 20 24 89.4 8876732. 68351760. 0.1390 > > 20 21 89.1 8780558. 67941296. 0.1390 > > 20 19 88.5 39924512. 280068256. 0.1530 > > 17 19 92.9 371385600. 509824768. 0.1530 > > 17 18 96.4 394707616. 358144416. 0.1230 > > 17 16 90.0 446916736. 883243840. 0.1360 > > 15 16 98.9 1051905920. 370290400. 0.1430 > > 14 15 100.8 520221760. 522257472. 0.1530 > > 13 14 128.2 1139173888. 3275473920. 0.1390 > > 13 11 155.0 2786396928. 3396753920. 0.1390 > > 11 12 151.7 1220930176. 2911329792. 0.1090 > > 9 11 161.5 369404096. 342864. 0.1390 > > 9 10 135.8 2190610944. 1502276608. 0.1090 > > 7 8 91.7 148944928. 1389486464. 0.1000 > > 6 9 150.6 497182528. 4613532672. 0.1390 > > 6 7 168.3 1652069120. 3562507776. 0.1360 > > 4 5 165.5 55138408. 449667456. 0.1000 > > 3 6 169.0 1702803200. 4615812096. 0.1390 > > 3 4 124.7 198457328. 2500093184. 0.1360 > > 13 1 158.1 1042088320. 3730094848. 0.1390 > > Wrote pdb files with previous and current coordinates > > Please I need your help what should I do in this case? > > Best regards, > > Safa > > -- > > gmx-users mailing listgmx-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.
Re: [gmx-users] vacum simulation
Thank you very much On 2 May 2013 22:00, Justin Lemkul wrote: > > > On 5/2/13 8:57 AM, Souilem Safa wrote: > >> Thank you for your quick answer >> I have joined here my mdp file and the toplogy one also. >> > > The mailing list does not accept attachments. Please copy and paste the > text into an email. We may not need the whole topology, but a description > of what you're working with is important. If you are using some novel > molecule for which you've generated parameters, those can be a source of > problems. > > > Should I increase the time step? I'm sorry I'm new in MD >> >> > Increasing the timestep in the case of instabilities is the exact opposite > of what you should do. Please read the link I posted earlier. > > -Justin > > > >> >> On 2 May 2013 21:48, Erik Marklund wrote: >> >> You seem to be using a 2 fs time step. It's difficult to achieve stable >>> integration using 2 fs time steps in vacuum. Please provide more >>> information about your simulation parameters. >>> >>> Erik >>> >>> On 2 May 2013, at 14:40, Souilem Safa wrote: >>> >>> Dear Gromacs users , >>>> I did the simulation of a single molecule in vacum. I have choosed 10 ns >>>> which corresponds to 500 steps. I was checking the .log file >>>> >>> frequently. >>> >>>> I have noticed that the number of steps from 1938900 didn't increases. >>>> When I open a new tab with the top option, I see mdrun still existing. >>>> I have attached here the .log file and also some warnings that I saw >>>> when >>>> steps stop at 1938900 >>>> >>>> Step 1938969, time 3877.94 (ps) LINCS WARNING >>>> relative constraint deviation after LINCS: >>>> rms 12871303501.643789, max 33207281664.00 (between atoms 3 and 6) >>>> bonds that rotated more than 30 degrees: >>>> atom 1 atom 2 angle previous, current, constraint length >>>> 46 47 98.80.1406 3889.8669 0.1000 >>>> 45 46 79.4 10193.8799 10564.2393 0.1440 >>>> 43 44 79.60.1033 631.2256 0.1000 >>>> 42 45 80.1 10193.9062 11014.6123 0.1520 >>>> 42 43 93.50.1851 4970.4243 0.1440 >>>> 40 41 76.50.1009 184.9659 0.1000 >>>> 39 42 90.40.1819 5231.5186 0.1520 >>>> 39 40 100.00.1502 624.0559 0.1440 >>>> 37 38 97.10.1001 592.4050 0.1000 >>>> 36 37 81.40.1469 828.7896 0.1430 >>>> 35 39 88.60.1742 8071.4395 0.1520 >>>> 35 36 94.70.1861 8093.3452 0.1530 >>>> 35 34 92.9 8046.3804 17904.5762 0.1440 >>>> 33 45 78.0 26093.2402 332765.5000 0.1520 >>>> 33 34 94.6 26065.5371 330302.5625 0.1440 >>>> 29 30 74.4 190965.5938 1213272. 0.1360 >>>> 27 28 91.2 85465.0547 294693.5000 0.1430 >>>> 25 27 85.7 126649.9141 1143663.7500 0.1360 >>>> 25 26 107.7 116051.3750 805165.8125 0.1230 >>>> 24 29 102.8 1939418.3750 1702562.5000 0.1390 >>>> 24 25 101.0 1963544.3750 1402288.3750 0.1390 >>>> 22 23 97.9 345568.0625 1364901. 0.1530 >>>> 31 21 109.7 1948370.1250 7003795.5000 0.1390 >>>> 21 22 101.2 2108572.2500 6662917.5000 0.1390 >>>> 20 24 89.4 8876732. 68351760. 0.1390 >>>> 20 21 89.1 8780558. 67941296. 0.1390 >>>> 20 19 88.5 39924512. 280068256. 0.1530 >>>> 17 19 92.9 371385600. 509824768. 0.1530 >>>> 17 18 96.4 394707616. 358144416. 0.1230 >>>> 17 16 90.0 446916736. 883243840. 0.1360 >>>> 15 16 98.9 1051905920. 370290400. 0.1430 >>>> 14 15 100.8 520221760. 522257472. 0.1530 >>>> 13 14 128.2 1139173888. 3275473920. 0.1390 >>>> 13 11 155.0 2786396928. 3396753920. 0.1390 >>>> 11 12 151.7 1220930176. 2911329792. 0.1090 >>>> 9 11 161.5 369404096. 342864. 0.1390 >>
Re: [gmx-users] vacum simulation
Thank you for your quick answer I have joined here my mdp file and the toplogy one also. Should I increase the time step? I'm sorry I'm new in MD On 2 May 2013 21:48, Erik Marklund wrote: > You seem to be using a 2 fs time step. It's difficult to achieve stable > integration using 2 fs time steps in vacuum. Please provide more > information about your simulation parameters. > > Erik > > On 2 May 2013, at 14:40, Souilem Safa wrote: > > > Dear Gromacs users , > > I did the simulation of a single molecule in vacum. I have choosed 10 ns > > which corresponds to 500 steps. I was checking the .log file > frequently. > > I have noticed that the number of steps from 1938900 didn't increases. > > When I open a new tab with the top option, I see mdrun still existing. > > I have attached here the .log file and also some warnings that I saw when > > steps stop at 1938900 > > > > Step 1938969, time 3877.94 (ps) LINCS WARNING > > relative constraint deviation after LINCS: > > rms 12871303501.643789, max 33207281664.00 (between atoms 3 and 6) > > bonds that rotated more than 30 degrees: > > atom 1 atom 2 angle previous, current, constraint length > > 46 47 98.80.1406 3889.8669 0.1000 > > 45 46 79.4 10193.8799 10564.2393 0.1440 > > 43 44 79.60.1033 631.2256 0.1000 > > 42 45 80.1 10193.9062 11014.6123 0.1520 > > 42 43 93.50.1851 4970.4243 0.1440 > > 40 41 76.50.1009 184.9659 0.1000 > > 39 42 90.40.1819 5231.5186 0.1520 > > 39 40 100.00.1502 624.0559 0.1440 > > 37 38 97.10.1001 592.4050 0.1000 > > 36 37 81.40.1469 828.7896 0.1430 > > 35 39 88.60.1742 8071.4395 0.1520 > > 35 36 94.70.1861 8093.3452 0.1530 > > 35 34 92.9 8046.3804 17904.5762 0.1440 > > 33 45 78.0 26093.2402 332765.5000 0.1520 > > 33 34 94.6 26065.5371 330302.5625 0.1440 > > 29 30 74.4 190965.5938 1213272. 0.1360 > > 27 28 91.2 85465.0547 294693.5000 0.1430 > > 25 27 85.7 126649.9141 1143663.7500 0.1360 > > 25 26 107.7 116051.3750 805165.8125 0.1230 > > 24 29 102.8 1939418.3750 1702562.5000 0.1390 > > 24 25 101.0 1963544.3750 1402288.3750 0.1390 > > 22 23 97.9 345568.0625 1364901. 0.1530 > > 31 21 109.7 1948370.1250 7003795.5000 0.1390 > > 21 22 101.2 2108572.2500 6662917.5000 0.1390 > > 20 24 89.4 8876732. 68351760. 0.1390 > > 20 21 89.1 8780558. 67941296. 0.1390 > > 20 19 88.5 39924512. 280068256. 0.1530 > > 17 19 92.9 371385600. 509824768. 0.1530 > > 17 18 96.4 394707616. 358144416. 0.1230 > > 17 16 90.0 446916736. 883243840. 0.1360 > > 15 16 98.9 1051905920. 370290400. 0.1430 > > 14 15 100.8 520221760. 522257472. 0.1530 > > 13 14 128.2 1139173888. 3275473920. 0.1390 > > 13 11 155.0 2786396928. 3396753920. 0.1390 > > 11 12 151.7 1220930176. 2911329792. 0.1090 > > 9 11 161.5 369404096. 342864. 0.1390 > > 9 10 135.8 2190610944. 1502276608. 0.1090 > > 7 8 91.7 148944928. 1389486464. 0.1000 > > 6 9 150.6 497182528. 4613532672. 0.1390 > > 6 7 168.3 1652069120. 3562507776. 0.1360 > > 4 5 165.5 55138408. 449667456. 0.1000 > > 3 6 169.0 1702803200. 4615812096. 0.1390 > > 3 4 124.7 198457328. 2500093184. 0.1360 > > 13 1 158.1 1042088320. 3730094848. 0.1390 > > Wrote pdb files with previous and current coordinates > > Please I need your help what should I do in this case? > > Best regards, > > Safa > > -- > > gmx-users mailing listgmx-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/Mailin
[gmx-users] vacum simulation
Dear Gromacs users , I did the simulation of a single molecule in vacum. I have choosed 10 ns which corresponds to 500 steps. I was checking the .log file frequently. I have noticed that the number of steps from 1938900 didn't increases. When I open a new tab with the top option, I see mdrun still existing. I have attached here the .log file and also some warnings that I saw when steps stop at 1938900 Step 1938969, time 3877.94 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 12871303501.643789, max 33207281664.00 (between atoms 3 and 6) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 46 47 98.80.1406 3889.8669 0.1000 45 46 79.4 10193.8799 10564.2393 0.1440 43 44 79.60.1033 631.2256 0.1000 42 45 80.1 10193.9062 11014.6123 0.1520 42 43 93.50.1851 4970.4243 0.1440 40 41 76.50.1009 184.9659 0.1000 39 42 90.40.1819 5231.5186 0.1520 39 40 100.00.1502 624.0559 0.1440 37 38 97.10.1001 592.4050 0.1000 36 37 81.40.1469 828.7896 0.1430 35 39 88.60.1742 8071.4395 0.1520 35 36 94.70.1861 8093.3452 0.1530 35 34 92.9 8046.3804 17904.5762 0.1440 33 45 78.0 26093.2402 332765.5000 0.1520 33 34 94.6 26065.5371 330302.5625 0.1440 29 30 74.4 190965.5938 1213272. 0.1360 27 28 91.2 85465.0547 294693.5000 0.1430 25 27 85.7 126649.9141 1143663.7500 0.1360 25 26 107.7 116051.3750 805165.8125 0.1230 24 29 102.8 1939418.3750 1702562.5000 0.1390 24 25 101.0 1963544.3750 1402288.3750 0.1390 22 23 97.9 345568.0625 1364901. 0.1530 31 21 109.7 1948370.1250 7003795.5000 0.1390 21 22 101.2 2108572.2500 6662917.5000 0.1390 20 24 89.4 8876732. 68351760. 0.1390 20 21 89.1 8780558. 67941296. 0.1390 20 19 88.5 39924512. 280068256. 0.1530 17 19 92.9 371385600. 509824768. 0.1530 17 18 96.4 394707616. 358144416. 0.1230 17 16 90.0 446916736. 883243840. 0.1360 15 16 98.9 1051905920. 370290400. 0.1430 14 15 100.8 520221760. 522257472. 0.1530 13 14 128.2 1139173888. 3275473920. 0.1390 13 11 155.0 2786396928. 3396753920. 0.1390 11 12 151.7 1220930176. 2911329792. 0.1090 9 11 161.5 369404096. 342864. 0.1390 9 10 135.8 2190610944. 1502276608. 0.1090 7 8 91.7 148944928. 1389486464. 0.1000 6 9 150.6 497182528. 4613532672. 0.1390 6 7 168.3 1652069120. 3562507776. 0.1360 4 5 165.5 55138408. 449667456. 0.1000 3 6 169.0 1702803200. 4615812096. 0.1390 3 4 124.7 198457328. 2500093184. 0.1360 13 1 158.1 1042088320. 3730094848. 0.1390 Wrote pdb files with previous and current coordinates Please I need your help what should I do in this case? Best regards, Safa -- gmx-users mailing listgmx-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
[gmx-users] interfacial-tension-interface simulation
Dear Gromacs users, I'm simulating a water-oil interface. From litterature interfacial tension is determined from pressure tensors as follows:1/2 (Pz - (px+py)/2))*Lz Where Pz, Px and Py are the pressure tensors in the different axis. I did a NPT simulation step and I want to check my interfacial tension value. Should I calculate the interfacial tension in every step and take the average interfacial tension for all the steps or should I take the average of the presssure tensors from all the steps and calculate the interfacial tension which will be only one value? Because it gives different values. Can any one help me in that? thanks -- gmx-users mailing listgmx-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
Re: [gmx-users] How to fix interfacial tension in NPT
Thank you for your reply :) I will look further On 25 April 2013 23:18, Justin Lemkul wrote: > > > On 4/25/13 9:10 AM, Souilem Safa wrote: > >> Dear Justin, >> Please I want to ask you for the calculation of interfacial tension from >> the formula : 1/2 (Pz - (px+py)/2))*Lz >> Should I calculate the interfacial tension in every step and take the >> average interfacial tension for all the steps or should I take the average >> of the presssure tensors from all the steps and calculate the interfacial >> tension which will be only one value? Because it gives different values. >> > > Beyond my area of expertise. Maybe someone who does this kind of work can > answer this. > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing listgmx-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
Re: [gmx-users] How to fix interfacial tension in NPT
Dear Justin, Please I want to ask you for the calculation of interfacial tension from the formula : 1/2 (Pz - (px+py)/2))*Lz Should I calculate the interfacial tension in every step and take the average interfacial tension for all the steps or should I take the average of the presssure tensors from all the steps and calculate the interfacial tension which will be only one value? Because it gives different values. Thank you very much On 22 April 2013 20:48, Souilem Safa wrote: > Dear Justin, > Thank you very much, that is very kind of you :) > > > > On 22 April 2013 19:42, Justin Lemkul wrote: > >> >> >> On 4/21/13 10:37 PM, Souilem Safa wrote: >> >>> Dear Justin, >>> >>> Thanks for your quick reply. >>> I used Gromos 96 force field, I found it well reproduce triglycerides >>> properties (A. Brasiello et al., 2010). I choose 53a6, I thought it is >>> the >>> updated one but I'm not sure if it well reproduce the the surface tension >>> properties . I found recently one paper simulating >>> triglyceride-phospholipid-**water membrane (G. Henneré et al., 2009), >>> they >>> use united atom force field for simulation. >>> Which force field do you think it is better , I'm sorry I have limited >>> knowledge about it since I'm just beginner in MD simulation. >>> >> >> My advice would be to find a study that has been shown to produce the >> types of data you are interested in, then try to reproduce it exactly. If >> you can do that, move on to your systems using the same force field. Only >> then can you sort out whether your results are due to some error that you >> are making (and I did note an important mistake below) or due to the >> limitations of the force field itself. >> >> -Justin >> >> On 22 April 2013 10:37, Justin Lemkul wrote: >>> >>> >>>> >>>> On 4/21/13 9:30 PM, Souilem Safa wrote: >>>> >>>> Dear Justin, >>>>> Thank you for your answer, I'm sorry for delay to reply. Actually I'm >>>>> running a simulation of oil-water interface. I'm using Gromos 53a6 >>>>> force >>>>> field which is usually used for triglycerides. after semiisotropic and >>>>> MD >>>>> step I still have around 40 mN.m-1 interfacial tension which is pretty >>>>> far >>>>> from my experimental value. Following is my mdp file for NPT step. >>>>> I would be very grateful if you can help me to solve this issue >>>>> >>>>> >>>> Do you have any reason to believe that 53A6 should reproduce quantities >>>> like surface tension? I haven't seen such a demonstration before, >>>> though I >>>> admit I haven't actively gone looking. The cutoffs you are using are >>>> incorrect for strict use of 53A6; that could be a contributing factor to >>>> your problems. >>>> >>>> -Justin >>>> >>>> title = NPT equilibration >>>> >>>>> ; Run parameters >>>>> integrator = md; leap-frog integrator >>>>> nsteps = 25; 2 *25 = 500 ps >>>>> dt = 0.002 ; 2 fs >>>>> ; Output control >>>>> nstxout = 500 ; save coordinates every 1 ps >>>>> nstvout = 100 ; save velocities every 0.2 ps >>>>> nstenergy = 100 ; save energies every 0.2 ps >>>>> nstlog = 100 ; update log file every 0.2 ps >>>>> ; Bond parameters >>>>> continuation= yes ; Restarting after NVT >>>>> constraint_algorithm = lincs; holonomic constraints >>>>> constraints = all-bonds ; all bonds (even heavy atom-H bonds) >>>>> constrained >>>>> lincs_iter = 2 ; accuracy of LINCS >>>>> lincs_order = 2 ; also related to accuracy >>>>> ; Neighborsearching >>>>> ns_type = grid ; search neighboring grid cells >>>>> nstlist = 5 ; 10 fs >>>>> rlist = 1.0 ; short-range neighborlist cutoff (in >>>>> nm) >>>>> rcoulomb= 1.0 ; short-range electrostatic cutoff (in >>>>> nm) >>>>> rvdw= 1.0 ; short-range van der Waals cutoff (in
Re: [gmx-users] How to fix interfacial tension in NPT
Dear Justin, Thank you very much, that is very kind of you :) On 22 April 2013 19:42, Justin Lemkul wrote: > > > On 4/21/13 10:37 PM, Souilem Safa wrote: > >> Dear Justin, >> >> Thanks for your quick reply. >> I used Gromos 96 force field, I found it well reproduce triglycerides >> properties (A. Brasiello et al., 2010). I choose 53a6, I thought it is the >> updated one but I'm not sure if it well reproduce the the surface tension >> properties . I found recently one paper simulating >> triglyceride-phospholipid-**water membrane (G. Henneré et al., 2009), >> they >> use united atom force field for simulation. >> Which force field do you think it is better , I'm sorry I have limited >> knowledge about it since I'm just beginner in MD simulation. >> > > My advice would be to find a study that has been shown to produce the > types of data you are interested in, then try to reproduce it exactly. If > you can do that, move on to your systems using the same force field. Only > then can you sort out whether your results are due to some error that you > are making (and I did note an important mistake below) or due to the > limitations of the force field itself. > > -Justin > > On 22 April 2013 10:37, Justin Lemkul wrote: >> >> >>> >>> On 4/21/13 9:30 PM, Souilem Safa wrote: >>> >>> Dear Justin, >>>> Thank you for your answer, I'm sorry for delay to reply. Actually I'm >>>> running a simulation of oil-water interface. I'm using Gromos 53a6 force >>>> field which is usually used for triglycerides. after semiisotropic and >>>> MD >>>> step I still have around 40 mN.m-1 interfacial tension which is pretty >>>> far >>>> from my experimental value. Following is my mdp file for NPT step. >>>> I would be very grateful if you can help me to solve this issue >>>> >>>> >>> Do you have any reason to believe that 53A6 should reproduce quantities >>> like surface tension? I haven't seen such a demonstration before, >>> though I >>> admit I haven't actively gone looking. The cutoffs you are using are >>> incorrect for strict use of 53A6; that could be a contributing factor to >>> your problems. >>> >>> -Justin >>> >>> title = NPT equilibration >>> >>>> ; Run parameters >>>> integrator = md; leap-frog integrator >>>> nsteps = 25; 2 *25 = 500 ps >>>> dt = 0.002 ; 2 fs >>>> ; Output control >>>> nstxout = 500 ; save coordinates every 1 ps >>>> nstvout = 100 ; save velocities every 0.2 ps >>>> nstenergy = 100 ; save energies every 0.2 ps >>>> nstlog = 100 ; update log file every 0.2 ps >>>> ; Bond parameters >>>> continuation= yes ; Restarting after NVT >>>> constraint_algorithm = lincs; holonomic constraints >>>> constraints = all-bonds ; all bonds (even heavy atom-H bonds) >>>> constrained >>>> lincs_iter = 2 ; accuracy of LINCS >>>> lincs_order = 2 ; also related to accuracy >>>> ; Neighborsearching >>>> ns_type = grid ; search neighboring grid cells >>>> nstlist = 5 ; 10 fs >>>> rlist = 1.0 ; short-range neighborlist cutoff (in >>>> nm) >>>> rcoulomb= 1.0 ; short-range electrostatic cutoff (in >>>> nm) >>>> rvdw= 1.0 ; short-range van der Waals cutoff (in >>>> nm) >>>> ; Electrostatics >>>> coulombtype = PME ; Particle Mesh Ewald for long-range >>>> electrostatics >>>> pme_order = 4 ; cubic interpolation >>>> fourierspacing = 0.16 ; grid spacing for FFT >>>> ; Temperature coupling is on >>>> tcoupl = V-rescale ; modified Berendsen thermostat >>>> tc-grps = SOL TRI ; two coupling groups - more accurate >>>> tau_t = 0.1 0.1 ; time constant, in ps >>>> ref_t = 300 300 ; reference temperature, one for each >>>> group, in K >>>> ; Pressure coupling is on >>>> pcoupl = parrinello-Rahman ; Pressure coupling on in NPT >>>> pcoupltype
Re: [gmx-users] How to fix interfacial tension in NPT
Dear Justin, Thanks for your quick reply. I used Gromos 96 force field, I found it well reproduce triglycerides properties (A. Brasiello et al., 2010). I choose 53a6, I thought it is the updated one but I'm not sure if it well reproduce the the surface tension properties . I found recently one paper simulating triglyceride-phospholipid-water membrane (G. Henneré et al., 2009), they use united atom force field for simulation. Which force field do you think it is better , I'm sorry I have limited knowledge about it since I'm just beginner in MD simulation. Many thanks On 22 April 2013 10:37, Justin Lemkul wrote: > > > On 4/21/13 9:30 PM, Souilem Safa wrote: > >> Dear Justin, >> Thank you for your answer, I'm sorry for delay to reply. Actually I'm >> running a simulation of oil-water interface. I'm using Gromos 53a6 force >> field which is usually used for triglycerides. after semiisotropic and MD >> step I still have around 40 mN.m-1 interfacial tension which is pretty far >> from my experimental value. Following is my mdp file for NPT step. >> I would be very grateful if you can help me to solve this issue >> > > Do you have any reason to believe that 53A6 should reproduce quantities > like surface tension? I haven't seen such a demonstration before, though I > admit I haven't actively gone looking. The cutoffs you are using are > incorrect for strict use of 53A6; that could be a contributing factor to > your problems. > > -Justin > > title = NPT equilibration >> ; Run parameters >> integrator = md; leap-frog integrator >> nsteps = 25; 2 *25 = 500 ps >> dt = 0.002 ; 2 fs >> ; Output control >> nstxout = 500 ; save coordinates every 1 ps >> nstvout = 100 ; save velocities every 0.2 ps >> nstenergy = 100 ; save energies every 0.2 ps >> nstlog = 100 ; update log file every 0.2 ps >> ; Bond parameters >> continuation= yes ; Restarting after NVT >> constraint_algorithm = lincs; holonomic constraints >> constraints = all-bonds ; all bonds (even heavy atom-H bonds) >> constrained >> lincs_iter = 2 ; accuracy of LINCS >> lincs_order = 2 ; also related to accuracy >> ; Neighborsearching >> ns_type = grid ; search neighboring grid cells >> nstlist = 5 ; 10 fs >> rlist = 1.0 ; short-range neighborlist cutoff (in nm) >> rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) >> rvdw= 1.0 ; short-range van der Waals cutoff (in nm) >> ; Electrostatics >> coulombtype = PME ; Particle Mesh Ewald for long-range >> electrostatics >> pme_order = 4 ; cubic interpolation >> fourierspacing = 0.16 ; grid spacing for FFT >> ; Temperature coupling is on >> tcoupl = V-rescale ; modified Berendsen thermostat >> tc-grps = SOL TRI ; two coupling groups - more accurate >> tau_t = 0.1 0.1 ; time constant, in ps >> ref_t = 300 300 ; reference temperature, one for each >> group, in K >> ; Pressure coupling is on >> pcoupl = parrinello-Rahman ; Pressure coupling on in NPT >> pcoupltype = semiisotropic ; uniform scaling of box vectors >> tau_p = 1.0 1.0 ; time constant, in ps >> ref_p = 1.0 1.0 ; reference pressure, in bar >> compressibility = 0 4.5e-5; isothermal compressibility x,y axis/z >> axis bar^-1 >> refcoord_scaling = com >> ; Periodic boundary conditions >> pbc = xyz ; 3-D PBC >> ; Dispersion correction >> DispCorr= enerpres ; account for cut-off vdW scheme >> ; Velocity generation >> gen_vel = no; Velocity generation is off >> >> >> >> >> On 19 April 2013 03:28, Justin Lemkul wrote: >> >> >>> >>> On 4/18/13 10:51 AM, Souilem Safa wrote: >>> >>> Dear Gromacs users, >>>> I have runned a semiisotropic NPT simulation for a membrane, I have >>>> fixed >>>> the pressure in x and y axis and I varied it only in z axis to keep a >>>> stable interface. But after simulation the obtained interfacial tension >>>> is >>>> far bigger than the experimental value. Experimental is 27 mN.m-1 and >>>> the >>>> simulated one was around
Re: [gmx-users] How to fix interfacial tension in NPT
Dear Justin, Thank you for your answer, I'm sorry for delay to reply. Actually I'm running a simulation of oil-water interface. I'm using Gromos 53a6 force field which is usually used for triglycerides. after semiisotropic and MD step I still have around 40 mN.m-1 interfacial tension which is pretty far from my experimental value. Following is my mdp file for NPT step. I would be very grateful if you can help me to solve this issue title = NPT equilibration ; Run parameters integrator = md; leap-frog integrator nsteps = 25; 2 *25 = 500 ps dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= yes ; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 2 ; accuracy of LINCS lincs_order = 2 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = SOL TRI ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of box vectors tau_p = 1.0 1.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, in bar compressibility = 0 4.5e-5; isothermal compressibility x,y axis/z axis bar^-1 refcoord_scaling = com ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= enerpres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off On 19 April 2013 03:28, Justin Lemkul wrote: > > > On 4/18/13 10:51 AM, Souilem Safa wrote: > >> Dear Gromacs users, >> I have runned a semiisotropic NPT simulation for a membrane, I have fixed >> the pressure in x and y axis and I varied it only in z axis to keep a >> stable interface. But after simulation the obtained interfacial tension is >> far bigger than the experimental value. Experimental is 27 mN.m-1 and the >> simulated one was around 38 mN.m-1. >> I will be very grateful if you can suggest me which parameters should I >> check in order to regulate the interfacial tension value. >> > > You haven't posted your .mdp file or even stated what force field you're > using. Is your force field designed to reproduce such surface tension > values? The results are only as good as the model itself, and your usage > of it. > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing listgmx-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
[gmx-users] How to fix interfacial tension in NPT
Dear Gromacs users, I have runned a semiisotropic NPT simulation for a membrane, I have fixed the pressure in x and y axis and I varied it only in z axis to keep a stable interface. But after simulation the obtained interfacial tension is far bigger than the experimental value. Experimental is 27 mN.m-1 and the simulated one was around 38 mN.m-1. I will be very grateful if you can suggest me which parameters should I check in order to regulate the interfacial tension value. Thank you very much -- gmx-users mailing listgmx-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
