Re: [gmx-users] a suitable forcefield for ions
Thanks Justin. I can only find atoms in ffnonbonded.itp in Amber ff. Where should I search for ions parameters in Amber ff? On Wed, May 25, 2016 at 4:01 PM, mah maz wrote: > Thanks Erik. I found nonbonded parameters for atoms only in Amber ff. Can > I use them for ions or they are already for ions? > eg. for Na sigma= 0.332 and epsilon=0.0115. Does it mean that we can use > thIS sigma and epsilon for Na+? > > On Wed, May 25, 2016 at 2:11 PM, mah maz wrote: > >> Hi all, >> >> i need forcefield parameters for ions. can anyone tell me which >> forcefield contains ions? can i do ion simulations with amber ff? >> >> Thank you >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] a suitable forcefield for ions
Thanks Erik. I found nonbonded parameters for atoms only in Amber ff. Can I use them for ions or they are already for ions? eg. for Na sigma= 0.332 and epsilon=0.0115. Does it mean that we can use thIS sigma and epsilon for Na+? On Wed, May 25, 2016 at 2:11 PM, mah maz wrote: > Hi all, > > i need forcefield parameters for ions. can anyone tell me which forcefield > contains ions? can i do ion simulations with amber ff? > > Thank you > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] a suitable forcefield for ions
Hi all, i need forcefield parameters for ions. can anyone tell me which forcefield contains ions? can i do ion simulations with amber ff? Thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Electric field unit
Seems rational! Thank you very much David. On Thu, Jan 14, 2016 at 7:20 PM, mah maz wrote: > Thank you David but it still seems conflicting to me. V/nm and V/m are 100 > times different! If it is in V/nm then force unit should be wrong! > > On Thu, Jan 14, 2016 at 12:20 PM, mah maz wrote: > >> Hi David, >> >> In the manual 4.6.7, Page8. It seems logical since the force unit is in >> KJ/mol.nm. And it can roughly be deduced from ions movements. >> What is the use of FIELDFAC in src code then? >> >> thank you. >> >> On Thu, Jan 14, 2016 at 10:54 AM, mah maz wrote: >> >>> Dear users, >>> >>> What is the electric field unit in gromacs? In the manual it is KJ/mol. >>> nm.e but in the source code I encountered V/nm which is about 100 times >>> KJ/mol.nm.e. >>> >>> Thank you. >>> >> >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Electric field unit
Thank you David but it still seems conflicting to me. V/nm and V/m are 100 times different! If it is in V/nm then force unit should be wrong! On Thu, Jan 14, 2016 at 12:20 PM, mah maz wrote: > Hi David, > > In the manual 4.6.7, Page8. It seems logical since the force unit is in KJ > /mol.nm. And it can roughly be deduced from ions movements. > What is the use of FIELDFAC in src code then? > > thank you. > > On Thu, Jan 14, 2016 at 10:54 AM, mah maz wrote: > >> Dear users, >> >> What is the electric field unit in gromacs? In the manual it is KJ/mol.nm.e >> but in the source code I encountered V/nm which is about 100 times KJ/mol >> .nm.e. >> >> Thank you. >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Electric field unit
Hi David, In the manual 4.6.7, Page8. It seems logical since the force unit is in KJ/ mol.nm. And it can roughly be deduced from ions movements. What is the use of FIELDFAC in src code then? thank you. On Thu, Jan 14, 2016 at 10:54 AM, mah maz wrote: > Dear users, > > What is the electric field unit in gromacs? In the manual it is KJ/mol.nm.e > but in the source code I encountered V/nm which is about 100 times KJ/mol. > nm.e. > > Thank you. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] necessary input files during simulation
Hi Tsjerk, Thank you very much. On Thu, Jan 14, 2016 at 10:46 AM, mah maz wrote: > Dear users, > > I deleted my input files(.gro,.mdp,.top,.ndx..) before the simulation is > over by mistake. However, it is still running. Which files should be > present to the end of a run? > > Thank you. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Electric field unit
Dear users, What is the electric field unit in gromacs? In the manual it is KJ/mol.nm.e but in the source code I encountered V/nm which is about 100 times KJ/mol.nm.e. Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] necessary input files during simulation
Dear users, I deleted my input files(.gro,.mdp,.top,.ndx..) before the simulation is over by mistake. However, it is still running. Which files should be present to the end of a run? Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] extracting coordinates from traj.xtc
And also, if I want velocities for every step what can I do? Thanks! On Sun, Dec 6, 2015 at 11:19 AM, mah maz wrote: > Thank you. I tested gmxdump and also trjconv -dump and compared traj.trr > and traj.xtc. You are right both have the same data. I just need the > coordinates to be readable a printable in a file now. Although I can write > a program to extract the coordinates from gmxdump the way I need, it > seems a bit time consuming. And I couldn't find a way yet! Is there a > command like g_traj -f traj.trr -ox to print coordinates from traj.xtc? > Thanks! > > On Thu, Dec 3, 2015 at 8:27 PM, mah maz wrote: > >> Thanks Justin! I checked the run and it seemed ok. The fact is, the data >> I get by g_traj -f traj.trr -ox is reasonable (although I didnt set nstxout >> it was set every 100 step by default), while the same command with g_traj >> -f traj.xtc -ox gives wrong coordinates. Since I need coordinates for every >> step I need to extract them from traj.xtc. Can you suggest any ways? >> >> Thank you! >> >> On Tue, Dec 1, 2015 at 4:51 PM, mah maz wrote: >> >>> Thank you Justin. I expected that only water molecules are written in >>> .xtc but all the others are there! g_traj -f traj.xtc -ox gives numbers >>> like 1.64e-318 for all frames! How can I get real coordinates from .xtc? >>> Thanks! >>> >>> On Tue, Dec 1, 2015 at 10:34 AM, mah maz wrote: >>> >>>> Dear all, >>>> I have some problems extracting data from traj.xtc. The command " g_ >>>> traj -s -ox" doesn't give reasonable coordinates. I tried "trjconv" >>>> but again couldn't get any results. Note that I have nstxtcout = 1 >>>> and xtc_grps = water in my .mdp file. >>>> Any help is appreciated. >>>> Thank you! >>>> >>> >>> >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] extracting coordinates from traj.xtc
Thank you. I tested gmxdump and also trjconv -dump and compared traj.trr and traj.xtc. You are right both have the same data. I just need the coordinates to be readable a printable in a file now. Although I can write a program to extract the coordinates from gmxdump the way I need, it seems a bit time consuming. And I couldn't find a way yet! Is there a command like g_traj -f traj.trr -ox to print coordinates from traj.xtc? Thanks! On Thu, Dec 3, 2015 at 8:27 PM, mah maz wrote: > Thanks Justin! I checked the run and it seemed ok. The fact is, the data I > get by g_traj -f traj.trr -ox is reasonable (although I didnt set nstxout > it was set every 100 step by default), while the same command with g_traj > -f traj.xtc -ox gives wrong coordinates. Since I need coordinates for every > step I need to extract them from traj.xtc. Can you suggest any ways? > > Thank you! > > On Tue, Dec 1, 2015 at 4:51 PM, mah maz wrote: > >> Thank you Justin. I expected that only water molecules are written in >> .xtc but all the others are there! g_traj -f traj.xtc -ox gives numbers >> like 1.64e-318 for all frames! How can I get real coordinates from .xtc? >> Thanks! >> >> On Tue, Dec 1, 2015 at 10:34 AM, mah maz wrote: >> >>> Dear all, >>> I have some problems extracting data from traj.xtc. The command " g_traj >>> -s -ox" doesn't give reasonable coordinates. I tried "trjconv" but >>> again couldn't get any results. Note that I have nstxtcout = 1 and xtc_ >>> grps = water in my .mdp file. >>> Any help is appreciated. >>> Thank you! >>> >> >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] extracting coordinates from traj.xtc
Thanks Justin! I checked the run and it seemed ok. The fact is, the data I get by g_traj -f traj.trr -ox is reasonable (although I didnt set nstxout it was set every 100 step by default), while the same command with g_traj -f traj.xtc -ox gives wrong coordinates. Since I need coordinates for every step I need to extract them from traj.xtc. Can you suggest any ways? Thank you! On Tue, Dec 1, 2015 at 4:51 PM, mah maz wrote: > Thank you Justin. I expected that only water molecules are written in .xtc > but all the others are there! g_traj -f traj.xtc -ox gives numbers like > 1.64e-318 for all frames! How can I get real coordinates from .xtc? > Thanks! > > On Tue, Dec 1, 2015 at 10:34 AM, mah maz wrote: > >> Dear all, >> I have some problems extracting data from traj.xtc. The command " g_traj >> -s -ox" doesn't give reasonable coordinates. I tried "trjconv" but again >> couldn't get any results. Note that I have nstxtcout = 1 and xtc_grps = >> water in my .mdp file. >> Any help is appreciated. >> Thank you! >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] extracting coordinates from traj.xtc
Thank you Justin. I expected that only water molecules are written in .xtc but all the others are there! g_traj -f traj.xtc -ox gives numbers like 1.64e-318 for all frames! How can I get real coordinates from .xtc? Thanks! On Tue, Dec 1, 2015 at 10:34 AM, mah maz wrote: > Dear all, > I have some problems extracting data from traj.xtc. The command " g_traj > -s -ox" doesn't give reasonable coordinates. I tried "trjconv" but again > couldn't get any results. Note that I have nstxtcout = 1 and xtc_grps = > water in my .mdp file. > Any help is appreciated. > Thank you! > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] extracting coordinates from traj.xtc
Dear all, I have some problems extracting data from traj.xtc. The command " g_traj -s -ox" doesn't give reasonable coordinates. I tried "trjconv" but again couldn't get any results. Note that I have nstxtcout = 1 and xtc_grps = water in my .mdp file. Any help is appreciated. Thank you! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC
I thought so :D Thanks! On Thu, Oct 8, 2015 at 9:37 AM, mah maz wrote: > Hi Mark > > Thank you. I suppose grid can be used without PBC specially when the > system is in vacuum. > There are some parameters in the .mdp file that I haven't defined and I > don't want them to be applied during simulation. However in the mdout.mdp > They are present eg. gen-seed, emtol, ewald-rtol, Do they play a role > in the simulation? > > Thanks! > > On Mon, Oct 5, 2015 at 2:26 PM, mah maz wrote: > >> Hi Mark, >> Thanks. It seems the default is pbc =xyz. But my question is if I don't >> use PBC, can I use grid, or grid is only meaningful when PBC is defined? >> >> On Mon, Oct 5, 2015 at 11:07 AM, mah maz wrote: >> >>> Dear users, >>> >>> If I dont define pbc=no, what is the default type for gromacs? Is it >>> right if I dont use pbc=no in my system while using grid for ns-type? >>> >>> thank you. >>> >> >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC
Hi Mark Thank you. I suppose grid can be used without PBC specially when the system is in vacuum. There are some parameters in the .mdp file that I haven't defined and I don't want them to be applied during simulation. However in the mdout.mdp They are present eg. gen-seed, emtol, ewald-rtol, Do they play a role in the simulation? Thanks! On Mon, Oct 5, 2015 at 2:26 PM, mah maz wrote: > Hi Mark, > Thanks. It seems the default is pbc =xyz. But my question is if I don't > use PBC, can I use grid, or grid is only meaningful when PBC is defined? > > On Mon, Oct 5, 2015 at 11:07 AM, mah maz wrote: > >> Dear users, >> >> If I dont define pbc=no, what is the default type for gromacs? Is it >> right if I dont use pbc=no in my system while using grid for ns-type? >> >> thank you. >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC
Hi Mark, Thanks. It seems the default is pbc =xyz. But my question is if I don't use PBC, can I use grid, or grid is only meaningful when PBC is defined? On Mon, Oct 5, 2015 at 11:07 AM, mah maz wrote: > Dear users, > > If I dont define pbc=no, what is the default type for gromacs? Is it right > if I dont use pbc=no in my system while using grid for ns-type? > > thank you. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PBC
Dear users, If I dont define pbc=no, what is the default type for gromacs? Is it right if I dont use pbc=no in my system while using grid for ns-type? thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] topology parameters
Dear users, Are resnr, residue, moleculetype, system and molecules names in .top file important? I have a CNT containing water molecules. I can see weather I assign CNT to all the molecules as residue names Or CNT and water, results are the same. Also if I use 1 for CNT as resdnr and 2 for water Or 1 for all of them I get the same results! Are they only names or something else eg. type is important in this case? Thanks! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] segmentation fault
Dear all, what is the solution for the segmentation fault after applying electric field? when I enter 1 for number of cosines mdrun doesnt start with segmentation fault error. does it mean that i can write any numbers as number of cosines and have stationary electric field or should i enter 1 only? thank you! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] segmentation fault
Dear all, for applying electric field in gromacs-4.5.5 I should enter 3 numbers. The first one is number of cosines that should be 1. any number smaller than 1 is acceptable but when I use 1, grompp is done but mdrun doesnt start with the following error: segmentation fault. What should I do? Is it because of the version I use? thank you! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] calculating electric field force
Dear all, I want to calculate the force caused by applying electric field in my system. I used g_traj -f tarj.xtc -of but it doesn't work. Does "-of" give external force? Are there any options to calculate the force from electric field? Thank you! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] installation errors
Thanks Mark! I could install it at last. I installed it in a desired directory not in root, used --enable-shared and --disable-float. that was the only way it was installed! and I should say I tried from all versions 5 to 4 and finally the one without errors was 4.5.5! (with fftw-3.3.4) I have 2 questions now: is it ok not to have gromacs installed in root? when I want to run is it necessary to have the file in the directory installed? and does double precision work the same as single?(I can see _d after commands) thanks alot On Mon, Jun 22, 2015 at 11:14 PM, mah maz wrote: > Thanks Parvez! but it was not the solution. do you have any other ideas to > help? > > On Sun, Jun 21, 2015 at 1:42 PM, mah maz wrote: > >> Dear all, >> I am trying to install a new version of gromacs(rather than rpm) on my >> system. I apply these commands:(in root while im superuser) >> tar -xzvf fftw-3.3.4.tar.gz >> cd fftw-3.3.4 >> ./configure --enable-float --enable-threads >> make >> make install >> >> and for gromacs: >> >> tar -xzvf gromacs-4.5.5.tar.gz >> cd gromacs-4.5.5 >> ./configure >> make >> after this command the following errors occur: >> can not be used when making a shared object >> recompile with -fPIC >> /usr/local/lib64/libfftw3.a:couldnt read symbols:bad value >> collect2: error: ld returned 1 exit status >> make[3]:***[libmd.la] error1 >> make[3]: leaving directory '/gromacs-4.5.5/src/mdlib >> make[2]: [all-recursive] error1 >> make[2]: leaving directory '/gromacs-4.5.5/src >> make[1]: error2 >> make[1]: leaving directory '/gromacs-4.5.5/src >> make***[all-recursive] error1 >> what should i do? is it because of the incompatibility of the >> fftw version and gromacs version? >> thanks! >> >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] installation errors
Thanks Parvez! but it was not the solution. do you have any other ideas to help? On Sun, Jun 21, 2015 at 1:42 PM, mah maz wrote: > Dear all, > I am trying to install a new version of gromacs(rather than rpm) on my > system. I apply these commands:(in root while im superuser) > tar -xzvf fftw-3.3.4.tar.gz > cd fftw-3.3.4 > ./configure --enable-float --enable-threads > make > make install > > and for gromacs: > > tar -xzvf gromacs-4.5.5.tar.gz > cd gromacs-4.5.5 > ./configure > make > after this command the following errors occur: > can not be used when making a shared object > recompile with -fPIC > /usr/local/lib64/libfftw3.a:couldnt read symbols:bad value > collect2: error: ld returned 1 exit status > make[3]:***[libmd.la] error1 > make[3]: leaving directory '/gromacs-4.5.5/src/mdlib > make[2]: [all-recursive] error1 > make[2]: leaving directory '/gromacs-4.5.5/src > make[1]: error2 > make[1]: leaving directory '/gromacs-4.5.5/src > make***[all-recursive] error1 > what should i do? is it because of the incompatibility of the > fftw version and gromacs version? > thanks! > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] installation errors
Dear all, I am trying to install a new version of gromacs(rather than rpm) on my system. I apply these commands:(in root while im superuser) tar -xzvf fftw-3.3.4.tar.gz cd fftw-3.3.4 ./configure --enable-float --enable-threads make make install and for gromacs: tar -xzvf gromacs-4.5.5.tar.gz cd gromacs-4.5.5 ./configure make after this command the following errors occur: can not be used when making a shared object recompile with -fPIC /usr/local/lib64/libfftw3.a:couldnt read symbols:bad value collect2: error: ld returned 1 exit status make[3]:***[libmd.la] error1 make[3]: leaving directory '/gromacs-4.5.5/src/mdlib make[2]: [all-recursive] error1 make[2]: leaving directory '/gromacs-4.5.5/src make[1]: error2 make[1]: leaving directory '/gromacs-4.5.5/src make***[all-recursive] error1 what should i do? is it because of the incompatibility of the fftw version and gromacs version? thanks! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] .mdp parameters source codes
It worked Justin. So many thanks! In the RPM version there is a lack of these source codes. Can I copy them from other versions? Cheers! On Sat, Jun 13, 2015 at 11:17 PM, mah maz wrote: > dear all, > I really need to know where i can find files that are written in C format > for .mdp parameters like thermostat, cutoffs and electric fields. I > searched in the source files and couldnt find anything. can anyone help me? > thanks! > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] .mdp parameters source codes
dear all, I really need to know where i can find files that are written in C format for .mdp parameters like thermostat, cutoffs and electric fields. I searched in the source files and couldnt find anything. can anyone help me? thanks! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] files related to commands in C or FORTRAN
Thank you very much Justin, Stephane. I found them. Where can I find .mdp parameters related files eg. thermostat code or electric field? On Fri, Jun 12, 2015 at 11:27 PM, mah maz wrote: > hi Justin, > in the gromacs website i can see different versions, regressiontests and > xdrs. which one should i download? > my question is about a code written for each command eg. msd calculation. > where can i find it? > thank you! > > On Fri, Jun 12, 2015 at 11:06 PM, mah maz wrote: > >> dear all, >> >> i want to find files that are probably written in C, C++ or fortran >> format for commands in gromacs. i tried root/usr/share/gromacs but there >> are only a few files, not all of them. note that the version i installed is >> a rpm one. where can i find them? >> >> thanks! >> >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] files related to commands in C or FORTRAN
hi Justin, in the gromacs website i can see different versions, regressiontests and xdrs. which one should i download? my question is about a code written for each command eg. msd calculation. where can i find it? thank you! On Fri, Jun 12, 2015 at 11:06 PM, mah maz wrote: > dear all, > > i want to find files that are probably written in C, C++ or fortran format > for commands in gromacs. i tried root/usr/share/gromacs but there are only > a few files, not all of them. note that the version i installed is a rpm > one. where can i find them? > > thanks! > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] files related to commands in C or FORTRAN
dear all, i want to find files that are probably written in C, C++ or fortran format for commands in gromacs. i tried root/usr/share/gromacs but there are only a few files, not all of them. note that the version i installed is a rpm one. where can i find them? thanks! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] RDF
Thanks Justin! I cant find so much details in the manual; there are only general facts. does g_density give partial density? On Mon, May 18, 2015 at 11:25 AM, mah maz wrote: > Hi Justin > The fact is I want to calculate water density in the system. If I select > group1: oxygen and group2: oxygen, g_rdf command gives me very large > numbers. Is it the number of atoms that should be changed to g/cm3? > Besides, what does it calculate, each O is a reference atom during > calculation? > Thanks a lot! > > On Sun, May 17, 2015 at 2:17 PM, mah maz wrote: > >> Dear all, >> I want to calculate the radial distribution function of water molecules >> in my system. I use g_rdf -f traj.xtc -n -o. It gives me large numbers >> which is not logical I suppose. Is it meaningful if I separate oxygen and >> hydrogen atoms in the index file and calculate the RDF for O-O atoms? Is >> reference atom necessary to get RDF? >> Thanks! >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] RDF
Hi Justin The fact is I want to calculate water density in the system. If I select group1: oxygen and group2: oxygen, g_rdf command gives me very large numbers. Is it the number of atoms that should be changed to g/cm3? Besides, what does it calculate, each O is a reference atom during calculation? Thanks a lot! On Sun, May 17, 2015 at 2:17 PM, mah maz wrote: > Dear all, > I want to calculate the radial distribution function of water molecules in > my system. I use g_rdf -f traj.xtc -n -o. It gives me large numbers which > is not logical I suppose. Is it meaningful if I separate oxygen and > hydrogen atoms in the index file and calculate the RDF for O-O atoms? Is > reference atom necessary to get RDF? > Thanks! > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] RDF
Dear all, I want to calculate the radial distribution function of water molecules in my system. I use g_rdf -f traj.xtc -n -o. It gives me large numbers which is not logical I suppose. Is it meaningful if I separate oxygen and hydrogen atoms in the index file and calculate the RDF for O-O atoms? Is reference atom necessary to get RDF? Thanks! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] atom freezing during simulation
Hi Justin, Unfortunately, I am looking at the right atoms! Coordinates of the frozen atoms are different from their initial ones and they have non-zero velocities. I set up the .mdp file as follows: freezegrps = frz1 frz2 freezdim = x y z x y z Is it the correct way of setting up frozen groups? Thank you! On Sun, May 3, 2015 at 9:47 AM, mah maz wrote: > Dear all, > > I need to freeze some atoms in my system not to move during simulation. I > used freezegrps and freezdim options but after simulation, I can see that > the fixed atoms also moved and their coordinates changed. What can I do to > fix their positions? Should I couple them with thermostat and assign low > temperatures to avoid their motion? > > Thanks! > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] atom freezing during simulation
Dear all, I need to freeze some atoms in my system not to move during simulation. I used freezegrps and freezdim options but after simulation, I can see that the fixed atoms also moved and their coordinates changed. What can I do to fix their positions? Should I couple them with thermostat and assign low temperatures to avoid their motion? Thanks! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] simultaneous runs
Thank you very much Justin! it was helpful as usual. On Sun, Apr 5, 2015 at 9:40 AM, mah maz wrote: > Dear all, > I performed 2 runs one after the other. Then, I performed those 2 runs > simultaneously(no special commands were applied, I just used different > terminals with mdrun -v command) but in different directories. Results > (like msd and energies) were expected to be nearly the same. but they are > completely different. Does it mean that we cant perform several runs > simultaneously? > Thanks! > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] simultaneous runs
Dear all, I performed 2 runs one after the other. Then, I performed those 2 runs simultaneously(no special commands were applied, I just used different terminals with mdrun -v command) but in different directories. Results (like msd and energies) were expected to be nearly the same. but they are completely different. Does it mean that we cant perform several runs simultaneously? Thanks! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] forcefield error for atoms
Thanks Justin! my system is a CNT but I need to insert some atoms in it with no bonds. The best way I found is to make a .pdb and .gro files of the newly constructed system and then without the use of g_x2top command, I added anything needed to the .top file which was made previously without the inserted atoms for the pure CNT system. changes in the .n2t file were also considered including atom introduction. It worked! Cheers On Thu, Mar 26, 2015 at 1:34 PM, mah maz wrote: > Hi Justin, > Thank you! I checked the coordinates and I think there's nothing wrong > with them. The problem might be from the .n2t file. I have some atoms > without any bonds to other atoms in my system. So, in the .n2t file I > assign 0 for bonds to other atoms. And it again stops with the same error > while making the topology file. How can I get rid of this error? > Cheers! > > On Tue, Mar 24, 2015 at 9:00 PM, mah maz wrote: > >> Hi Justin, >> Thanks for your reply. As you guessed correctly, for making a topology >> file I used "g_x2top -f file.gro -o file.top -ff forcefield -noparam". >> I have a CNT system and I thought I should use g_x2top instead of >> pdb2gmx command. If I'm right, what may cause this error and what would be >> the solution? >> Thanks! >> >> On Mon, Mar 23, 2015 at 12:41 AM, mah maz wrote: >> >>> Dear all, >>> I need to insert some atoms (without any bonds to other atoms) or even >>> ions in my system. I have created the .pdb, and .gro files, but when I >>> try to generate the .top file it stops with the following error: " >>> forcefield not found for atoms with 0 bonds". Is there a way to solve this >>> problem? >>> Thanks! >>> >> >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] forcefield error for atoms
Hi Justin, Thank you! I checked the coordinates and I think there's nothing wrong with them. The problem might be from the .n2t file. I have some atoms without any bonds to other atoms in my system. So, in the .n2t file I assign 0 for bonds to other atoms. And it again stops with the same error while making the topology file. How can I get rid of this error? Cheers! On Tue, Mar 24, 2015 at 9:00 PM, mah maz wrote: > Hi Justin, > Thanks for your reply. As you guessed correctly, for making a topology > file I used "g_x2top -f file.gro -o file.top -ff forcefield -noparam". I > have a CNT system and I thought I should use g_x2top instead of pdb2gmx > command. If I'm right, what may cause this error and what would be the > solution? > Thanks! > > On Mon, Mar 23, 2015 at 12:41 AM, mah maz wrote: > >> Dear all, >> I need to insert some atoms (without any bonds to other atoms) or even >> ions in my system. I have created the .pdb, and .gro files, but when I >> try to generate the .top file it stops with the following error: " >> forcefield not found for atoms with 0 bonds". Is there a way to solve this >> problem? >> Thanks! >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] forcefield error for atoms
Hi Justin, Thanks for your reply. As you guessed correctly, for making a topology file I used "g_x2top -f file.gro -o file.top -ff forcefield -noparam". I have a CNT system and I thought I should use g_x2top instead of pdb2gmx command. If I'm right, what may cause this error and what would be the solution? Thanks! On Mon, Mar 23, 2015 at 12:41 AM, mah maz wrote: > Dear all, > I need to insert some atoms (without any bonds to other atoms) or even > ions in my system. I have created the .pdb, and .gro files, but when I > try to generate the .top file it stops with the following error: " > forcefield not found for atoms with 0 bonds". Is there a way to solve this > problem? > Thanks! > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] forcefield error for atoms
Dear all, I need to insert some atoms (without any bonds to other atoms) or even ions in my system. I have created the .pdb, and .gro files, but when I try to generate the .top file it stops with the following error: " forcefield not found for atoms with 0 bonds". Is there a way to solve this problem? Thanks! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] trajectory film
Hi Justin, Thank you very much! On Thu, Mar 12, 2015 at 9:53 AM, mah maz wrote: > Dear all, > I have a question probably not related to this mailing list! I want to see > a film of an output trajectory via VMD. I tried the .trr file by the > appropriate format in VMD, it shows that the frames are being constructed > and rendering is complete but nothing can be seen. Is there a problem with > my .trr file? Can anyone help me in this regard? > thanks! > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] trajectory film
Dear all, I have a question probably not related to this mailing list! I want to see a film of an output trajectory via VMD. I tried the .trr file by the appropriate format in VMD, it shows that the frames are being constructed and rendering is complete but nothing can be seen. Is there a problem with my .trr file? Can anyone help me in this regard? thanks! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] high temperature
I see. I just don't understand the difference between these results. Useful as always. Many thanks! On Tue, Mar 3, 2015 at 10:57 PM, mah maz wrote: > Hi Justin, > That's the .mdp file. > dt = 0.0001 > tinit = 0 > nsteps = 10 > nstxout = 1000 > nstvout = 1000 > nstfout = 0 > nstlog = 1000 > nstenergy = 1000 > nstlist = 5 > ns_type = grid > rlist = 0.2 > coulombtype = reaction-field-zero > epsilon_rf = 0 > rcoulomb= 0.1 > rvdw= 0.2 > vdwtype = cutoff > pbc = no > integrator = md-vv > Tcoupl = nose-hoover > tau_t = 0.1 0.1 > ref_t = 300 300 > tc_grps = CNT water > > unwanted temperatures from the 2nd computer are: > > 0.00 > 569.41912 > 487.04663 > 428.94406 > 548.68127 > 406.10748 > 533.70324 > 487.37088 > 456.60519 > 452.93588 > 442.06088 > 463.36178 > 472.95275 > 502.68411 > 421.56173 > 492.36709 > 537.82879 > 483.68277 > 475.07675 > 494.39749 > 452.90744 > 494.20474 > 474.09298 > 482.93124 > 487.88989 > 509.66070 > 454.61138 > 453.75927 > 460.47540 > 454.69632 > 505.48443 > 485.54705 > 472.73492 > 460.27398 > 493.66903 > 480.78952 > 482.55233 > 470.91381 > 496.23098 > 484.82730 > 455.13006 > 469.39798 > 506.39819 > 479.32211 > 500.88891 > 485.77325 > 489.26815 > 476.03207 > 469.77734 > 466.56793 > 493.62396 > 482.78839 > 470.33157 > 462.17074 > 477.09906 > 470.76757 > 489.31381 > 486.11468 > 475.64276 > 471.49072 > 482.00595 > 485.38873 > 480.53643 > 475.79977 > 469.22253 > 488.72970 > 481.01446 > 493.13934 > 486.96911 > 481.62371 > 469.96023 > 488.82580 > 482.96316 > 476.70632 > 487.02590 > 487.53659 > 476.29904 > 472.44818 > 479.97314 > 477.46865 > 473.29275 > 469.93447 > 474.75863 > 472.98861 > 478.05273 > 486.17233 > 480.43383 > 475.78836 > 482.39563 > 480.41461 > 476.73916 > 490.22122 > 482.99255 > 478.54370 > 480.67889 > 478.16925 > 479.58938 > 474.47232 > 484.70156 > 484.90008 > 481.15057 > - > wanted temperatures from the 1st computer: > > 0.00 > 326.691895 > 294.764709 > 298.554596 > 282.649414 > 307.463135 > 291.600189 > 300.543671 > 299.999359 > 297.054443 > 305.510986 > 303.078583 > 299.970428 > 299.137207 > 297.810272 > 298.365875 > 298.783813 > 301.805695 > 303.370575 > 300.340332 > 301.656372 > 299.389984 > 300.836243 > 296.977936 > 298.827637 > 299.861847 > 300.578522 > 296.483398 > 296.462646 > 302.666473 > 297.978180 > 304.715515 > 300.773193 > 300.172913 > 307.178711 > 298.444183 > 312.749542 > 302.172089 > 301.957428 > 303.820526 > 303.579712 > 296.149872 > 296.983826 > 303.023834 > 299.992371 > 299.144897 > 295.73 > 305.296722 > 304.449219 > 309.249756 > 302.303375 > 304.800293 > 301.949646 > 302.895538 > 307.148254 > 298.277069 > 302.761719 > 296.531281 > 296.709900 > 298.417542 > 300.391022 > 297.293732 > 299.136353 > 290.259125 > 299.269531 > 305.229675 > 301.938751 > 301.106384 > 301.689117 > 295.249969 > 298.655914 > 296.441071 > 300.491364 > 304.039795 > 301.149384 > 295.906250 > 300.652557 > 296.303467 > 300.960083 > 304.725067 > 291.927765 > 303.753845 > 300.202393 > 294.915588 > 297.580017 > 302.882233 > 300.872406 > 306.164551 > 299.459473 > 300.940948 > 306.348328 > 299.031982 > 299.465942 > 297.603119 > 301.168304 > 305.233917 > 292.175751 > 304.453491 > 300.391571 > 303.061188 > 302.262146 > Hope they are the data you wanted. > Thanks for your time and help. > > On Tue, Mar 3, 2015 at 10:30 PM, mah maz wrote: > >> Dear Justin, >> You are right, but I'm not asking about conditions in .mdp. I wanted to >> ask how a result(of temperature here) can be different from one computer to >> another while I have even the same GROMACS versions in both? I copied >> the .gro .top .mdp .ndx and .ff from the computer I got the good results >> to another, but I see about 150K difference in temperature! >> Your help is greatly appreciated. >> Thanks! >> >> On Tue, Mar 3, 2015 at 10:41 AM, mah maz wrote: >> >>> Hi Justin, >>> I performed the run with the reacti
Re: [gmx-users] high temperature
Hi Justin, That's the .mdp file. dt = 0.0001 tinit = 0 nsteps = 10 nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstlist = 5 ns_type = grid rlist = 0.2 coulombtype = reaction-field-zero epsilon_rf = 0 rcoulomb= 0.1 rvdw= 0.2 vdwtype = cutoff pbc = no integrator = md-vv Tcoupl = nose-hoover tau_t = 0.1 0.1 ref_t = 300 300 tc_grps = CNT water unwanted temperatures from the 2nd computer are: 0.00 569.41912 487.04663 428.94406 548.68127 406.10748 533.70324 487.37088 456.60519 452.93588 442.06088 463.36178 472.95275 502.68411 421.56173 492.36709 537.82879 483.68277 475.07675 494.39749 452.90744 494.20474 474.09298 482.93124 487.88989 509.66070 454.61138 453.75927 460.47540 454.69632 505.48443 485.54705 472.73492 460.27398 493.66903 480.78952 482.55233 470.91381 496.23098 484.82730 455.13006 469.39798 506.39819 479.32211 500.88891 485.77325 489.26815 476.03207 469.77734 466.56793 493.62396 482.78839 470.33157 462.17074 477.09906 470.76757 489.31381 486.11468 475.64276 471.49072 482.00595 485.38873 480.53643 475.79977 469.22253 488.72970 481.01446 493.13934 486.96911 481.62371 469.96023 488.82580 482.96316 476.70632 487.02590 487.53659 476.29904 472.44818 479.97314 477.46865 473.29275 469.93447 474.75863 472.98861 478.05273 486.17233 480.43383 475.78836 482.39563 480.41461 476.73916 490.22122 482.99255 478.54370 480.67889 478.16925 479.58938 474.47232 484.70156 484.90008 481.15057 - wanted temperatures from the 1st computer: 0.00 326.691895 294.764709 298.554596 282.649414 307.463135 291.600189 300.543671 299.999359 297.054443 305.510986 303.078583 299.970428 299.137207 297.810272 298.365875 298.783813 301.805695 303.370575 300.340332 301.656372 299.389984 300.836243 296.977936 298.827637 299.861847 300.578522 296.483398 296.462646 302.666473 297.978180 304.715515 300.773193 300.172913 307.178711 298.444183 312.749542 302.172089 301.957428 303.820526 303.579712 296.149872 296.983826 303.023834 299.992371 299.144897 295.73 305.296722 304.449219 309.249756 302.303375 304.800293 301.949646 302.895538 307.148254 298.277069 302.761719 296.531281 296.709900 298.417542 300.391022 297.293732 299.136353 290.259125 299.269531 305.229675 301.938751 301.106384 301.689117 295.249969 298.655914 296.441071 300.491364 304.039795 301.149384 295.906250 300.652557 296.303467 300.960083 304.725067 291.927765 303.753845 300.202393 294.915588 297.580017 302.882233 300.872406 306.164551 299.459473 300.940948 306.348328 299.031982 299.465942 297.603119 301.168304 305.233917 292.175751 304.453491 300.391571 303.061188 302.262146 Hope they are the data you wanted. Thanks for your time and help. On Tue, Mar 3, 2015 at 10:30 PM, mah maz wrote: > Dear Justin, > You are right, but I'm not asking about conditions in .mdp. I wanted to > ask how a result(of temperature here) can be different from one computer to > another while I have even the same GROMACS versions in both? I copied the > .gro .top .mdp .ndx and .ff from the computer I got the good results to > another, but I see about 150K difference in temperature! > Your help is greatly appreciated. > Thanks! > > On Tue, Mar 3, 2015 at 10:41 AM, mah maz wrote: > >> Hi Justin, >> I performed the run with the reaction-field-zero as I said, but when I >> try to simulate it with exactly the same conditions on another computer it >> again gives me high temperatures! I again changed the conditions but it >> didn't work. Have you got any suggestions? >> Thank you! >> >> On Mon, Mar 2, 2015 at 10:08 PM, mah maz wrote: >> >>> Hi Justin, >>> So many thanks for your help. The problem was solved by changing cutoff >>> to reaction-field-zero and epsilon_rf=0. It just may need some >>> modifications for assigning right rvdw, rcoulomb and rlist. Thanks >>> again! >>> Cheers >>> >>> >>> >>> On Mon, Mar 2, 2015 at 7:03 PM, mah maz wrote: >>> >>>> Dear Justin, >>>> Thank you very much for your answer. Cutoffs are not set by exact >>>> studies and as you said they are arbitrary. Actually I don't know how to >>>> choose them for my system. I have CNT in water not vacuo. I tried >>>> rvdw=rcoulomb=rlist=0 but temperatures are still high. I studied the manual >>>> but don't know how to set them. Have you got any ideas to help? >>>> thanks! >>>> Cheers >>>> >>>> On Sun, Mar 1, 2015 at 8:55 PM, mah maz wrote: >>>
Re: [gmx-users] high temperature
Dear Justin, You are right, but I'm not asking about conditions in .mdp. I wanted to ask how a result(of temperature here) can be different from one computer to another while I have even the same GROMACS versions in both? I copied the . gro .top .mdp .ndx and .ff from the computer I got the good results to another, but I see about 150K difference in temperature! Your help is greatly appreciated. Thanks! On Tue, Mar 3, 2015 at 10:41 AM, mah maz wrote: > Hi Justin, > I performed the run with the reaction-field-zero as I said, but when I try > to simulate it with exactly the same conditions on another computer it > again gives me high temperatures! I again changed the conditions but it > didn't work. Have you got any suggestions? > Thank you! > > On Mon, Mar 2, 2015 at 10:08 PM, mah maz wrote: > >> Hi Justin, >> So many thanks for your help. The problem was solved by changing cutoff >> to reaction-field-zero and epsilon_rf=0. It just may need some >> modifications for assigning right rvdw, rcoulomb and rlist. Thanks again! >> Cheers >> >> >> >> On Mon, Mar 2, 2015 at 7:03 PM, mah maz wrote: >> >>> Dear Justin, >>> Thank you very much for your answer. Cutoffs are not set by exact >>> studies and as you said they are arbitrary. Actually I don't know how to >>> choose them for my system. I have CNT in water not vacuo. I tried >>> rvdw=rcoulomb=rlist=0 but temperatures are still high. I studied the manual >>> but don't know how to set them. Have you got any ideas to help? >>> thanks! >>> Cheers >>> >>> On Sun, Mar 1, 2015 at 8:55 PM, mah maz wrote: >>> >>>> Dear Chaban, >>>> >>>> Thank you very much. Could you please explain more about the problem >>>> and how I may fix it? >>>> >>>> Cheers >>>> >>>> On Sun, Mar 1, 2015 at 11:16 AM, mah maz wrote: >>>> >>>>> Dear all, >>>>> >>>>> I have a CNT system. I have set the mdp file as follows, but the >>>>> temperature output is logically more than what I expected even in the >>>>> production step(around 500k). I have changed the mdp file several times >>>>> but >>>>> it doesn't work. What are the possible causes of problem? >>>>> Thank you! >>>>> dt = 0.0001 >>>>> tinit = 0 >>>>> nsteps = 200 >>>>> nstxout = 1000 >>>>> nstvout = 1000 >>>>> nstfout = 0 >>>>> nstlog = 1000 >>>>> nstenergy = 1000 >>>>> nstlist = 5 >>>>> ns_type = grid >>>>> rlist = 0.9 >>>>> coulombtype = cut-off >>>>> rcoulomb= 0.9 >>>>> rvdw= 0.9 >>>>> rvdw_switch = 0.5 >>>>> vdwtype = switch >>>>> pbc = no >>>>> integrator = md-vv >>>>> Tcoupl = nose-hoover >>>>> tau_t = 0.1 >>>>> ref_t = 300 >>>>> tc_grps = CNT >>>>> gen_temp= 300 >>>>> pcoupl = no >>>>> >>>>> >>>> >>> >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] high temperature
Hi Justin, I performed the run with the reaction-field-zero as I said, but when I try to simulate it with exactly the same conditions on another computer it again gives me high temperatures! I again changed the conditions but it didn't work. Have you got any suggestions? Thank you! On Mon, Mar 2, 2015 at 10:08 PM, mah maz wrote: > Hi Justin, > So many thanks for your help. The problem was solved by changing cutoff to > reaction-field-zero and epsilon_rf=0. It just may need some modifications > for assigning right rvdw, rcoulomb and rlist. Thanks again! > Cheers > > > > On Mon, Mar 2, 2015 at 7:03 PM, mah maz wrote: > >> Dear Justin, >> Thank you very much for your answer. Cutoffs are not set by exact studies >> and as you said they are arbitrary. Actually I don't know how to choose >> them for my system. I have CNT in water not vacuo. I tried >> rvdw=rcoulomb=rlist=0 but temperatures are still high. I studied the manual >> but don't know how to set them. Have you got any ideas to help? >> thanks! >> Cheers >> >> On Sun, Mar 1, 2015 at 8:55 PM, mah maz wrote: >> >>> Dear Chaban, >>> >>> Thank you very much. Could you please explain more about the problem and >>> how I may fix it? >>> >>> Cheers >>> >>> On Sun, Mar 1, 2015 at 11:16 AM, mah maz wrote: >>> >>>> Dear all, >>>> >>>> I have a CNT system. I have set the mdp file as follows, but the >>>> temperature output is logically more than what I expected even in the >>>> production step(around 500k). I have changed the mdp file several times but >>>> it doesn't work. What are the possible causes of problem? >>>> Thank you! >>>> dt = 0.0001 >>>> tinit = 0 >>>> nsteps = 200 >>>> nstxout = 1000 >>>> nstvout = 1000 >>>> nstfout = 0 >>>> nstlog = 1000 >>>> nstenergy = 1000 >>>> nstlist = 5 >>>> ns_type = grid >>>> rlist = 0.9 >>>> coulombtype = cut-off >>>> rcoulomb= 0.9 >>>> rvdw= 0.9 >>>> rvdw_switch = 0.5 >>>> vdwtype = switch >>>> pbc = no >>>> integrator = md-vv >>>> Tcoupl = nose-hoover >>>> tau_t = 0.1 >>>> ref_t = 300 >>>> tc_grps = CNT >>>> gen_temp= 300 >>>> pcoupl = no >>>> >>>> >>> >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] high temperature
Hi Justin, So many thanks for your help. The problem was solved by changing cutoff to reaction-field-zero and epsilon_rf=0. It just may need some modifications for assigning right rvdw, rcoulomb and rlist. Thanks again! Cheers On Mon, Mar 2, 2015 at 7:03 PM, mah maz wrote: > Dear Justin, > Thank you very much for your answer. Cutoffs are not set by exact studies > and as you said they are arbitrary. Actually I don't know how to choose > them for my system. I have CNT in water not vacuo. I tried > rvdw=rcoulomb=rlist=0 but temperatures are still high. I studied the manual > but don't know how to set them. Have you got any ideas to help? > thanks! > Cheers > > On Sun, Mar 1, 2015 at 8:55 PM, mah maz wrote: > >> Dear Chaban, >> >> Thank you very much. Could you please explain more about the problem and >> how I may fix it? >> >> Cheers >> >> On Sun, Mar 1, 2015 at 11:16 AM, mah maz wrote: >> >>> Dear all, >>> >>> I have a CNT system. I have set the mdp file as follows, but the >>> temperature output is logically more than what I expected even in the >>> production step(around 500k). I have changed the mdp file several times but >>> it doesn't work. What are the possible causes of problem? >>> Thank you! >>> dt = 0.0001 >>> tinit = 0 >>> nsteps = 200 >>> nstxout = 1000 >>> nstvout = 1000 >>> nstfout = 0 >>> nstlog = 1000 >>> nstenergy = 1000 >>> nstlist = 5 >>> ns_type = grid >>> rlist = 0.9 >>> coulombtype = cut-off >>> rcoulomb= 0.9 >>> rvdw= 0.9 >>> rvdw_switch = 0.5 >>> vdwtype = switch >>> pbc = no >>> integrator = md-vv >>> Tcoupl = nose-hoover >>> tau_t = 0.1 >>> ref_t = 300 >>> tc_grps = CNT >>> gen_temp= 300 >>> pcoupl = no >>> >>> >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] high temperature
Dear Justin, Thank you very much for your answer. Cutoffs are not set by exact studies and as you said they are arbitrary. Actually I don't know how to choose them for my system. I have CNT in water not vacuo. I tried rvdw=rcoulomb=rlist=0 but temperatures are still high. I studied the manual but don't know how to set them. Have you got any ideas to help? thanks! Cheers On Sun, Mar 1, 2015 at 8:55 PM, mah maz wrote: > Dear Chaban, > > Thank you very much. Could you please explain more about the problem and > how I may fix it? > > Cheers > > On Sun, Mar 1, 2015 at 11:16 AM, mah maz wrote: > >> Dear all, >> >> I have a CNT system. I have set the mdp file as follows, but the >> temperature output is logically more than what I expected even in the >> production step(around 500k). I have changed the mdp file several times but >> it doesn't work. What are the possible causes of problem? >> Thank you! >> dt = 0.0001 >> tinit = 0 >> nsteps = 200 >> nstxout = 1000 >> nstvout = 1000 >> nstfout = 0 >> nstlog = 1000 >> nstenergy = 1000 >> nstlist = 5 >> ns_type = grid >> rlist = 0.9 >> coulombtype = cut-off >> rcoulomb= 0.9 >> rvdw= 0.9 >> rvdw_switch = 0.5 >> vdwtype = switch >> pbc = no >> integrator = md-vv >> Tcoupl = nose-hoover >> tau_t = 0.1 >> ref_t = 300 >> tc_grps = CNT >> gen_temp= 300 >> pcoupl = no >> >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] high temperature
Dear Chaban, Thank you very much. Could you please explain more about the problem and how I may fix it? Cheers On Sun, Mar 1, 2015 at 11:16 AM, mah maz wrote: > Dear all, > > I have a CNT system. I have set the mdp file as follows, but the > temperature output is logically more than what I expected even in the > production step(around 500k). I have changed the mdp file several times but > it doesn't work. What are the possible causes of problem? > Thank you! > dt = 0.0001 > tinit = 0 > nsteps = 200 > nstxout = 1000 > nstvout = 1000 > nstfout = 0 > nstlog = 1000 > nstenergy = 1000 > nstlist = 5 > ns_type = grid > rlist = 0.9 > coulombtype = cut-off > rcoulomb= 0.9 > rvdw= 0.9 > rvdw_switch = 0.5 > vdwtype = switch > pbc = no > integrator = md-vv > Tcoupl = nose-hoover > tau_t = 0.1 > ref_t = 300 > tc_grps = CNT > gen_temp= 300 > pcoupl = no > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] high temperature
Dear all, I have a CNT system. I have set the mdp file as follows, but the temperature output is logically more than what I expected even in the production step(around 500k). I have changed the mdp file several times but it doesn't work. What are the possible causes of problem? Thank you! dt = 0.0001 tinit = 0 nsteps = 200 nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstlist = 5 ns_type = grid rlist = 0.9 coulombtype = cut-off rcoulomb= 0.9 rvdw= 0.9 rvdw_switch = 0.5 vdwtype = switch pbc = no integrator = md-vv Tcoupl = nose-hoover tau_t = 0.1 ref_t = 300 tc_grps = CNT gen_temp= 300 pcoupl = no -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] several runs
Dear Mark,Victor,Szilard So many thanks for your helpful comments! Cheers On Tue, Feb 24, 2015 at 11:10 PM, mah maz wrote: > Hi Justin, > Thank you for your answer! If you may help with any of these questions I > would be greatly grateful; > How can I understand if they were interfered? How is pinning? Any other > ways you can recommend? > > Thanks a lot > > On Tue, Feb 24, 2015 at 10:14 PM, mah maz wrote: > >> Is running simulations in several terminals problematic? >> >> On Tue, Feb 24, 2015 at 8:42 PM, mah maz wrote: >> >>> Dear all, >>> >>> How can I perform several simulations simultaneously (in linux)? >>> >>> thank you! >>> >> >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] several runs
Hi Justin, Thank you for your answer! If you may help with any of these questions I would be greatly grateful; How can I understand if they were interfered? How is pinning? Any other ways you can recommend? Thanks a lot On Tue, Feb 24, 2015 at 10:14 PM, mah maz wrote: > Is running simulations in several terminals problematic? > > On Tue, Feb 24, 2015 at 8:42 PM, mah maz wrote: > >> Dear all, >> >> How can I perform several simulations simultaneously (in linux)? >> >> thank you! >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] several runs
Is running simulations in several terminals problematic? On Tue, Feb 24, 2015 at 8:42 PM, mah maz wrote: > Dear all, > > How can I perform several simulations simultaneously (in linux)? > > thank you! > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] several runs
Dear all, How can I perform several simulations simultaneously (in linux)? thank you! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] electric fields
Dear David, I'm sorry for the delay in saying thank you! You saved me a great deal of time. However, I can apply only low omegas in my system(about 1(ps^-1)) while in your article omega is about 600(ps^-1). (I wonder if I'm right about the dimensions). have you got any ideas? Many thanks! On Sun, Feb 15, 2015 at 11:19 PM, mah maz wrote: > Dear Justin, David > > Thank you for your reply. > I have also seen not implemented yet as Justin said. > David, I hope your option E-xt works. But still I don't know if I should > supply its parameters the same as E-x or it would be different. > > Thanks a lot! > > On Sun, Feb 15, 2015 at 9:01 PM, mah maz wrote: > >> Hi all, >> I need to apply magnetic and also alternating electric field to my >> system, but I can't find any options. Can anyone help me? >> thanks! >> >> On Fri, Feb 13, 2015 at 8:44 PM, mah maz wrote: >> >>> Dear all, >>> What kinds of electric and magnetic fields are available in gromacs? Are >>> there any commands for discontinuous(alternating) fields? >>> thank you! >>> >> >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] electric fields
Dear Justin, David Thank you for your reply. I have also seen not implemented yet as Justin said. David, I hope your option E-xt works. But still I don't know if I should supply its parameters the same as E-x or it would be different. Thanks a lot! On Sun, Feb 15, 2015 at 9:01 PM, mah maz wrote: > Hi all, > I need to apply magnetic and also alternating electric field to my system, > but I can't find any options. Can anyone help me? > thanks! > > On Fri, Feb 13, 2015 at 8:44 PM, mah maz wrote: > >> Dear all, >> What kinds of electric and magnetic fields are available in gromacs? Are >> there any commands for discontinuous(alternating) fields? >> thank you! >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] electric fields
Hi all, I need to apply magnetic and also alternating electric field to my system, but I can't find any options. Can anyone help me? thanks! On Fri, Feb 13, 2015 at 8:44 PM, mah maz wrote: > Dear all, > What kinds of electric and magnetic fields are available in gromacs? Are > there any commands for discontinuous(alternating) fields? > thank you! > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] electric fields
Dear all, What kinds of electric and magnetic fields are available in gromacs? Are there any commands for discontinuous(alternating) fields? thank you! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] msd calculation
Dear All, I want to calculate msd for a group of atoms of my system in different directions (x, y and z). What is the exact difference between -type, -lateral and -ten in g_msd command? which one should I use? Thank you! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] coordinates file format
Dear Mark, That was a great deal of help. This time, I agree with your last sentence ;-) Thanks a lot! Cheers, Mah On Wed, Jan 28, 2015 at 2:23 PM, mah maz wrote: > Dear Mark, Erik > > Mark, thank you very much! I asked google and it didn't know either! ;-) > your code also didn't work in FORTRAN. I've searched and found out it is > not probably an easy task to read a .trr file and even .xtc in FORTRAN. > Have you got any other ideas? > Erik, It took me more than 5hrs to read it in FORTRAN and I couldn't > succeed! I'm not familiar with python. thanks anyway. > Regards, > Mah > > On Tue, Jan 27, 2015 at 12:31 PM, mah maz wrote: > >> Dear Justin and Mark, >> >> I think you are both right. >> >> I didn't get your last sentence Mark! What is a libxdrfile? >> >> Justin, The problem is I have so many atoms in the system. As I said the >> best format for reading data is to be like this: >> time x1 y1 z1 x2 y2 z2 ... xn yn zn >> 0 1 2 3 2 3 4 8 5 6 >> 0.1 >> 0.2 >> ... >> as you know the trajectory format is like this: >> >> (t=)0 x1 y1 z1 x2 y2 z2 x3 y3 z3 x4 y4 z4... >> x5 y5 z5 . x4000 y4000 z4000 >> (t=)0.1 x1 y1 z1 x2 y2 z2.. >> x5 y5 z5 ... x4000 y4000 z4 >> completely difficult and confusing for me and the program both! >> >> According to your points, I can come to the conclusion that changing the >> file format is not possible. >> I appreciate your help as usual. thanks alot! >> >> Cheers, >> Mah >> >> >> >> >> >> >> >> On Mon, Jan 26, 2015 at 8:01 PM, mah maz wrote: >> >>> Dear Mark, >>> >>> Thanks for your reply. I think it is not! I have 4000 atoms, the first >>> number is time, then 4000 x y and z: x1,y1,z1, x2, y2, z2, ,x4000, >>> y4000, z4000. They are following each other not in a special order. Then >>> the next time step starts with x1,y1,z1,,x4000, y4000, z4000. So, they >>> are not in a column as they are supposed to be. Can I do anything to a >>> result file to be in my preferable format? >>> >>> Many Thanks! >>> Regards, >>> Mah >>> >>> On Mon, Jan 26, 2015 at 12:08 PM, mah maz wrote: >>> >>>> Hi Mark, >>>> I want to have X Y Z of each atom for all time step apart from other >>>> atoms so that I can use them as data for programing; like this for >>>> instance: >>>> tx1 y1 z1 x2 y2 z2 >>>> 02.4 3.5 4.5 5.6 7.9 9.8 >>>> 0.1 5.5 6.7 8.9 >>>> ... >>>> in which 0 and 0.1 are time and the rest are x1 y1 z1 of the 1st atom >>>> and x2 y2 z2 are for the 2nd atom. >>>> Is it possible to get the file in a desired format? >>>> thank you! >>>> >>>> On Mon, Jan 26, 2015 at 11:54 AM, mah maz wrote: >>>> >>>>> Dear all, >>>>> >>>>> I have extracted a file of coordinates after a simulation with 100 >>>>> steps writen every 1000 steps, by "g_traj -s -ox" . The result is a file >>>>> in >>>>> which the first column is time and all coordinates are following it. Is >>>>> there a way that I can get coordinates of each time step in a more >>>>> classified way? >>>>> >>>>> Thanks! >>>>> >>>> >>>> >>> >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] coordinates file format
Dear Mark, Erik Mark, thank you very much! I asked google and it didn't know either! ;-) your code also didn't work in FORTRAN. I've searched and found out it is not probably an easy task to read a .trr file and even .xtc in FORTRAN. Have you got any other ideas? Erik, It took me more than 5hrs to read it in FORTRAN and I couldn't succeed! I'm not familiar with python. thanks anyway. Regards, Mah On Tue, Jan 27, 2015 at 12:31 PM, mah maz wrote: > Dear Justin and Mark, > > I think you are both right. > > I didn't get your last sentence Mark! What is a libxdrfile? > > Justin, The problem is I have so many atoms in the system. As I said the > best format for reading data is to be like this: > time x1 y1 z1 x2 y2 z2 ... xn yn zn > 0 1 2 3 2 3 4 8 5 6 > 0.1 > 0.2 > ... > as you know the trajectory format is like this: > > (t=)0 x1 y1 z1 x2 y2 z2 x3 y3 z3 x4 y4 z4... > x5 y5 z5 . x4000 y4000 z4000 > (t=)0.1 x1 y1 z1 x2 y2 z2.. > x5 y5 z5 ... x4000 y4000 z4 > completely difficult and confusing for me and the program both! > > According to your points, I can come to the conclusion that changing the > file format is not possible. > I appreciate your help as usual. thanks alot! > > Cheers, > Mah > > > > > > > > On Mon, Jan 26, 2015 at 8:01 PM, mah maz wrote: > >> Dear Mark, >> >> Thanks for your reply. I think it is not! I have 4000 atoms, the first >> number is time, then 4000 x y and z: x1,y1,z1, x2, y2, z2, ,x4000, >> y4000, z4000. They are following each other not in a special order. Then >> the next time step starts with x1,y1,z1,,x4000, y4000, z4000. So, they >> are not in a column as they are supposed to be. Can I do anything to a >> result file to be in my preferable format? >> >> Many Thanks! >> Regards, >> Mah >> >> On Mon, Jan 26, 2015 at 12:08 PM, mah maz wrote: >> >>> Hi Mark, >>> I want to have X Y Z of each atom for all time step apart from other >>> atoms so that I can use them as data for programing; like this for instance: >>> tx1 y1 z1 x2 y2 z2 >>> 02.4 3.5 4.5 5.6 7.9 9.8 >>> 0.1 5.5 6.7 8.9 >>> ... >>> in which 0 and 0.1 are time and the rest are x1 y1 z1 of the 1st atom >>> and x2 y2 z2 are for the 2nd atom. >>> Is it possible to get the file in a desired format? >>> thank you! >>> >>> On Mon, Jan 26, 2015 at 11:54 AM, mah maz wrote: >>> >>>> Dear all, >>>> >>>> I have extracted a file of coordinates after a simulation with 100 >>>> steps writen every 1000 steps, by "g_traj -s -ox" . The result is a file in >>>> which the first column is time and all coordinates are following it. Is >>>> there a way that I can get coordinates of each time step in a more >>>> classified way? >>>> >>>> Thanks! >>>> >>> >>> >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] coordinates file format
Dear Justin and Mark, I think you are both right. I didn't get your last sentence Mark! What is a libxdrfile? Justin, The problem is I have so many atoms in the system. As I said the best format for reading data is to be like this: time x1 y1 z1 x2 y2 z2 ... xn yn zn 0 1 2 3 2 3 4 8 5 6 0.1 0.2 ... as you know the trajectory format is like this: (t=)0 x1 y1 z1 x2 y2 z2 x3 y3 z3 x4 y4 z4... x5 y5 z5 . x4000 y4000 z4000 (t=)0.1 x1 y1 z1 x2 y2 z2.. x5 y5 z5 ... x4000 y4000 z4 completely difficult and confusing for me and the program both! According to your points, I can come to the conclusion that changing the file format is not possible. I appreciate your help as usual. thanks alot! Cheers, Mah On Mon, Jan 26, 2015 at 8:01 PM, mah maz wrote: > Dear Mark, > > Thanks for your reply. I think it is not! I have 4000 atoms, the first > number is time, then 4000 x y and z: x1,y1,z1, x2, y2, z2, ,x4000, > y4000, z4000. They are following each other not in a special order. Then > the next time step starts with x1,y1,z1,,x4000, y4000, z4000. So, they > are not in a column as they are supposed to be. Can I do anything to a > result file to be in my preferable format? > > Many Thanks! > Regards, > Mah > > On Mon, Jan 26, 2015 at 12:08 PM, mah maz wrote: > >> Hi Mark, >> I want to have X Y Z of each atom for all time step apart from other >> atoms so that I can use them as data for programing; like this for instance: >> tx1 y1 z1 x2 y2 z2 >> 02.4 3.5 4.5 5.6 7.9 9.8 >> 0.1 5.5 6.7 8.9 >> ... >> in which 0 and 0.1 are time and the rest are x1 y1 z1 of the 1st atom and >> x2 y2 z2 are for the 2nd atom. >> Is it possible to get the file in a desired format? >> thank you! >> >> On Mon, Jan 26, 2015 at 11:54 AM, mah maz wrote: >> >>> Dear all, >>> >>> I have extracted a file of coordinates after a simulation with 100 >>> steps writen every 1000 steps, by "g_traj -s -ox" . The result is a file in >>> which the first column is time and all coordinates are following it. Is >>> there a way that I can get coordinates of each time step in a more >>> classified way? >>> >>> Thanks! >>> >> >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] coordinates file format
Dear Mark, Thanks for your reply. I think it is not! I have 4000 atoms, the first number is time, then 4000 x y and z: x1,y1,z1, x2, y2, z2, ,x4000, y4000, z4000. They are following each other not in a special order. Then the next time step starts with x1,y1,z1,,x4000, y4000, z4000. So, they are not in a column as they are supposed to be. Can I do anything to a result file to be in my preferable format? Many Thanks! Regards, Mah On Mon, Jan 26, 2015 at 12:08 PM, mah maz wrote: > Hi Mark, > I want to have X Y Z of each atom for all time step apart from other atoms > so that I can use them as data for programing; like this for instance: > tx1 y1 z1 x2 y2 z2 > 02.4 3.5 4.5 5.6 7.9 9.8 > 0.1 5.5 6.7 8.9 > ... > in which 0 and 0.1 are time and the rest are x1 y1 z1 of the 1st atom and > x2 y2 z2 are for the 2nd atom. > Is it possible to get the file in a desired format? > thank you! > > On Mon, Jan 26, 2015 at 11:54 AM, mah maz wrote: > >> Dear all, >> >> I have extracted a file of coordinates after a simulation with 100 >> steps writen every 1000 steps, by "g_traj -s -ox" . The result is a file in >> which the first column is time and all coordinates are following it. Is >> there a way that I can get coordinates of each time step in a more >> classified way? >> >> Thanks! >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] coordinates file format
Hi Mark, I want to have X Y Z of each atom for all time step apart from other atoms so that I can use them as data for programing; like this for instance: tx1 y1 z1 x2 y2 z2 02.4 3.5 4.5 5.6 7.9 9.8 0.1 5.5 6.7 8.9 ... in which 0 and 0.1 are time and the rest are x1 y1 z1 of the 1st atom and x2 y2 z2 are for the 2nd atom. Is it possible to get the file in a desired format? thank you! On Mon, Jan 26, 2015 at 11:54 AM, mah maz wrote: > Dear all, > > I have extracted a file of coordinates after a simulation with 100 > steps writen every 1000 steps, by "g_traj -s -ox" . The result is a file in > which the first column is time and all coordinates are following it. Is > there a way that I can get coordinates of each time step in a more > classified way? > > Thanks! > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] coordinates file format
Dear all, I have extracted a file of coordinates after a simulation with 100 steps writen every 1000 steps, by "g_traj -s -ox" . The result is a file in which the first column is time and all coordinates are following it. Is there a way that I can get coordinates of each time step in a more classified way? Thanks! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] potential energy
Dear Bogdan, Actually I have generated CNT from a garphene sheet myself. The last question reflects that! Thanks alot for answering all the questions and useful points you mentioned. Regards, Mah On Tue, Jan 20, 2015 at 10:43 PM, mah maz wrote: > Dear Justin, > > Thank you very much for your beneficial analysis. The problem is not > solved completely but the situation is improved for sure. Your help is > always precious. > > Best Regards, > Mah > > On 1/16/15, mah maz wrote: > > Hi Justin, > > I haven't come to a conclusion yet and need your help! I attached a copy > of > > a typical g_energy -f ener.edr -o copied from terminal and an .mdp file. > > > > Bond18506.5 501625.68 -301.714 > > (kJ/mol) > > Angle 9839.32 13580.506 -30.2625 > > (kJ/mol) > > Proper Dih. 60199.3 23845.936106.894 > > (kJ/mol) > > LJ-14 40461.9 411748.27 -227.144 > > (kJ/mol) > > Coulomb-140 0 0 0 > > (kJ/mol) > > LJ (SR)-10117.72.6118.855 -3.85515 > > (kJ/mol) > > Coulomb (SR) -156.169 9 40.82335.6671 > > (kJ/mol) > > Potential118733 741142.65 -420.414 > > (kJ/mol) > > Kinetic En. 14932.17.3423.825 -50.1192 > > (kJ/mol) > > Total Energy 133665 811221.66 -470.533 > > (kJ/mol) > > Conserved En.180812 57121.277397.186 > > (kJ/mol) > > Temperature 295.064 0.148.37495 -0.990376 (K) > > Pressure -0.072961 0.17 17.163 -0.120159 > (bar) > > Vir-XX 4860.4521021707.326.9299 > > (kJ/mol) > > Vir-XY 4.732333.3 1176.9 -2.74323 > > (kJ/mol) > > Vir-XZ 3.180977.51907.36 4.2031 > > (kJ/mol) > > Vir-YX 4.731473.31176.89 -2.74818 > > (kJ/mol) > > Vir-YY 5388.86 39 5500.8202.824 > > (kJ/mol) > > Vir-YZ0.05093923.21101.973.89409 > > (kJ/mol) > > Vir-ZX 3.180897.51907.364.19967 > > (kJ/mol) > > Vir-ZY0.05142363.21101.973.89442 > > (kJ/mol) > > Vir-ZZ 4871.7620021686.431.3387 > > (kJ/mol) > > Pres-XX0.156061 0.2525.1574 -0.125195 > (bar) > > Pres-XY -0.00268517 0.00331.36879 0.00150158 > > (bar) > > Pres-XZ -0.00196111 0.00982.21263 -0.0154319 > > (bar) > > Pres-YX -0.00268417 0.00331.36879 0.00150732 > > (bar) > > Pres-YY -0.511872 0.0196.38934 -0.0849178 > (bar) > > Pres-YZ 0.000542369 0.00171.27895 0.00355122 > > (bar) > > Pres-ZX -0.00196102 0.00982.21263 -0.0154279 > > (bar) > > Pres-ZY 0.000541808 0.00171.27895 0.00355084 > > (bar) > > Pres-ZZ0.136928 0.2425.1334 -0.150365 > (bar) > > #Surf*SurfTen 8.815353.2359.945 -1.26863 > (bar > > nm) > > T-CNT 295.063 0.148.44198 -0.997647 (K) > > T-grp1 295.202 0.2138.5349 0.485478 (K) > > T-grp2294.688 0.3253.7236 -2.39488 (K) > > > > > > > > dt = 0.0001 > > tinit = 0 > > nsteps = 200 > > nstxout = 1000 > > nstvout = 1000 > > nstfout = 0 > > nstlog = 1000 > > nstenergy = 1000 > > nstlist = 5 > > ns_type = grid > > rlist = 0.9 > > coulombtype = cutoff > > rcoulomb= 0.9 > > rvdw= 0.9 > > pbc = xyz > > integrator = md-vv > > Tcoupl = nose-hoover > > tau_t = 0.1 0.1 0.1 > > ref_t = 295 295 295 > > tc_grps = CNT grp1 grp2 > > gen_temp= 295 > > > > Your answer to any of these questions would be a ton of help! &
Re: [gmx-users] potential energy
Dear Justin, Thank you very much for your beneficial analysis. The problem is not solved completely but the situation is improved for sure. Your help is always precious. Best Regards, Mah On 1/16/15, mah maz wrote: > Hi Justin, > I haven't come to a conclusion yet and need your help! I attached a copy of > a typical g_energy -f ener.edr -o copied from terminal and an .mdp file. > > Bond18506.5 501625.68 -301.714 > (kJ/mol) > Angle 9839.32 13580.506 -30.2625 > (kJ/mol) > Proper Dih. 60199.3 23845.936106.894 > (kJ/mol) > LJ-14 40461.9 411748.27 -227.144 > (kJ/mol) > Coulomb-140 0 0 0 > (kJ/mol) > LJ (SR)-10117.72.6118.855 -3.85515 > (kJ/mol) > Coulomb (SR) -156.169 9 40.82335.6671 > (kJ/mol) > Potential118733 741142.65 -420.414 > (kJ/mol) > Kinetic En. 14932.17.3423.825 -50.1192 > (kJ/mol) > Total Energy 133665 811221.66 -470.533 > (kJ/mol) > Conserved En.180812 57121.277397.186 > (kJ/mol) > Temperature 295.064 0.148.37495 -0.990376 (K) > Pressure -0.072961 0.17 17.163 -0.120159 (bar) > Vir-XX 4860.4521021707.326.9299 > (kJ/mol) > Vir-XY 4.732333.3 1176.9 -2.74323 > (kJ/mol) > Vir-XZ 3.180977.51907.36 4.2031 > (kJ/mol) > Vir-YX 4.731473.31176.89 -2.74818 > (kJ/mol) > Vir-YY 5388.86 39 5500.8202.824 > (kJ/mol) > Vir-YZ0.05093923.21101.973.89409 > (kJ/mol) > Vir-ZX 3.180897.51907.364.19967 > (kJ/mol) > Vir-ZY0.05142363.21101.973.89442 > (kJ/mol) > Vir-ZZ 4871.7620021686.431.3387 > (kJ/mol) > Pres-XX0.156061 0.2525.1574 -0.125195 (bar) > Pres-XY -0.00268517 0.00331.36879 0.00150158 > (bar) > Pres-XZ -0.00196111 0.00982.21263 -0.0154319 > (bar) > Pres-YX -0.00268417 0.00331.36879 0.00150732 > (bar) > Pres-YY -0.511872 0.0196.38934 -0.0849178 (bar) > Pres-YZ 0.000542369 0.00171.27895 0.00355122 > (bar) > Pres-ZX -0.00196102 0.00982.21263 -0.0154279 > (bar) > Pres-ZY 0.000541808 0.00171.27895 0.00355084 > (bar) > Pres-ZZ0.136928 0.2425.1334 -0.150365 (bar) > #Surf*SurfTen 8.815353.2359.945 -1.26863 (bar > nm) > T-CNT 295.063 0.148.44198 -0.997647 (K) > T-grp1 295.202 0.2138.5349 0.485478 (K) > T-grp2294.688 0.3253.7236 -2.39488 (K) > > > > dt = 0.0001 > tinit = 0 > nsteps = 200 > nstxout = 1000 > nstvout = 1000 > nstfout = 0 > nstlog = 1000 > nstenergy = 1000 > nstlist = 5 > ns_type = grid > rlist = 0.9 > coulombtype = cutoff > rcoulomb= 0.9 > rvdw= 0.9 > pbc = xyz > integrator = md-vv > Tcoupl = nose-hoover > tau_t = 0.1 0.1 0.1 > ref_t = 295 295 295 > tc_grps = CNT grp1 grp2 > gen_temp= 295 > > Your answer to any of these questions would be a ton of help! > These potential energies are the average ones, how can I get the final > potential of the system? Are average potentials good terms to decide if the > simulation was wrong? > Can the positive potentials be the effect of forcefield inappropriate > files? > The system is a CNT containing some solvent. Can positive potentials be the > reflection of the system's angle pressure not willing to reform from plane > graphene system? > > I would appreciate your help. Many thanks in advance! > Regards, > Mah > > > > > > On Sun, Jan 11, 2015 at 5:31 PM, mah maz wrote: > >> Hi Justin, >> That's right in the .edr I have more than these 4 terms, I just mentioned >> the terms related to energy of the system
Re: [gmx-users] potential energy
Hi Justin, I haven't come to a conclusion yet and need your help! I attached a copy of a typical g_energy -f ener.edr -o copied from terminal and an .mdp file. Bond18506.5 501625.68 -301.714 (kJ/mol) Angle 9839.32 13580.506 -30.2625 (kJ/mol) Proper Dih. 60199.3 23845.936106.894 (kJ/mol) LJ-14 40461.9 411748.27 -227.144 (kJ/mol) Coulomb-140 0 0 0 (kJ/mol) LJ (SR)-10117.72.6118.855 -3.85515 (kJ/mol) Coulomb (SR) -156.169 9 40.82335.6671 (kJ/mol) Potential118733 741142.65 -420.414 (kJ/mol) Kinetic En. 14932.17.3423.825 -50.1192 (kJ/mol) Total Energy 133665 811221.66 -470.533 (kJ/mol) Conserved En.180812 57121.277397.186 (kJ/mol) Temperature 295.064 0.148.37495 -0.990376 (K) Pressure -0.072961 0.17 17.163 -0.120159 (bar) Vir-XX 4860.4521021707.326.9299 (kJ/mol) Vir-XY 4.732333.3 1176.9 -2.74323 (kJ/mol) Vir-XZ 3.180977.51907.36 4.2031 (kJ/mol) Vir-YX 4.731473.31176.89 -2.74818 (kJ/mol) Vir-YY 5388.86 39 5500.8202.824 (kJ/mol) Vir-YZ0.05093923.21101.973.89409 (kJ/mol) Vir-ZX 3.180897.51907.364.19967 (kJ/mol) Vir-ZY0.05142363.21101.973.89442 (kJ/mol) Vir-ZZ 4871.7620021686.431.3387 (kJ/mol) Pres-XX0.156061 0.2525.1574 -0.125195 (bar) Pres-XY -0.00268517 0.00331.36879 0.00150158 (bar) Pres-XZ -0.00196111 0.00982.21263 -0.0154319 (bar) Pres-YX -0.00268417 0.00331.36879 0.00150732 (bar) Pres-YY -0.511872 0.0196.38934 -0.0849178 (bar) Pres-YZ 0.000542369 0.00171.27895 0.00355122 (bar) Pres-ZX -0.00196102 0.00982.21263 -0.0154279 (bar) Pres-ZY 0.000541808 0.00171.27895 0.00355084 (bar) Pres-ZZ0.136928 0.2425.1334 -0.150365 (bar) #Surf*SurfTen 8.815353.2359.945 -1.26863 (bar nm) T-CNT 295.063 0.148.44198 -0.997647 (K) T-grp1 295.202 0.2138.5349 0.485478 (K) T-grp2294.688 0.3253.7236 -2.39488 (K) dt = 0.0001 tinit = 0 nsteps = 200 nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstlist = 5 ns_type = grid rlist = 0.9 coulombtype = cutoff rcoulomb= 0.9 rvdw= 0.9 pbc = xyz integrator = md-vv Tcoupl = nose-hoover tau_t = 0.1 0.1 0.1 ref_t = 295 295 295 tc_grps = CNT grp1 grp2 gen_temp= 295 Your answer to any of these questions would be a ton of help! These potential energies are the average ones, how can I get the final potential of the system? Are average potentials good terms to decide if the simulation was wrong? Can the positive potentials be the effect of forcefield inappropriate files? The system is a CNT containing some solvent. Can positive potentials be the reflection of the system's angle pressure not willing to reform from plane graphene system? I would appreciate your help. Many thanks in advance! Regards, Mah On Sun, Jan 11, 2015 at 5:31 PM, mah maz wrote: > Hi Justin, > That's right in the .edr I have more than these 4 terms, I just mentioned > the terms related to energy of the system.The output file is a large one > not in a proper format to be sent, but can be attached if possible. > That was a great deal of help up to this point. > Thank you very much! > Regards, > Mah > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] potential energy
Hi Justin, That's right in the .edr I have more than these 4 terms, I just mentioned the terms related to energy of the system.The output file is a large one not in a proper format to be sent, but can be attached if possible. That was a great deal of help up to this point. Thank you very much! Regards, Mah -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] potential energy
some solvent in nanotube actually! What do you mean by various energy components? In the results, I just have terms for potential, kinetic, total energy and conserved energy which are all positive in all steps. On Sun, Jan 11, 2015 at 12:52 AM, mah maz wrote: > I see! You are right. But my system is a nanotube not in gas phase. Is it > possible in this case? > Thanks alot! > > On Sun, Jan 11, 2015 at 12:40 AM, mah maz wrote: > >> Thank you Justin! >> you mean we can have a stable system with positive potential and total >> energy? >> Regards, >> Mah >> >> On Sun, Jan 11, 2015 at 12:22 AM, mah maz wrote: >> >>> Dear all, >>> I wanted to know if the potential energy gained by "g_energy -f ener.edr >>> -o" the total potential energy of the system or partial ones like vdw >>> energy. If it is the total energy, to my knowledge it should be negative, >>> and its summation with the kinetic energy should be negative showing the >>> stability of the system. In my simulation, potential energy is positive and >>> the total energy is a big positive number, but no explosion happened. What >>> is the problem? >>> thank you! >>> >> >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] potential energy
I see! You are right. But my system is a nanotube not in gas phase. Is it possible in this case? Thanks alot! On Sun, Jan 11, 2015 at 12:40 AM, mah maz wrote: > Thank you Justin! > you mean we can have a stable system with positive potential and total > energy? > Regards, > Mah > > On Sun, Jan 11, 2015 at 12:22 AM, mah maz wrote: > >> Dear all, >> I wanted to know if the potential energy gained by "g_energy -f ener.edr >> -o" the total potential energy of the system or partial ones like vdw >> energy. If it is the total energy, to my knowledge it should be negative, >> and its summation with the kinetic energy should be negative showing the >> stability of the system. In my simulation, potential energy is positive and >> the total energy is a big positive number, but no explosion happened. What >> is the problem? >> thank you! >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] potential energy
Thank you Justin! you mean we can have a stable system with positive potential and total energy? Regards, Mah On Sun, Jan 11, 2015 at 12:22 AM, mah maz wrote: > Dear all, > I wanted to know if the potential energy gained by "g_energy -f ener.edr > -o" the total potential energy of the system or partial ones like vdw > energy. If it is the total energy, to my knowledge it should be negative, > and its summation with the kinetic energy should be negative showing the > stability of the system. In my simulation, potential energy is positive and > the total energy is a big positive number, but no explosion happened. What > is the problem? > thank you! > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] potential energy
Dear all, I wanted to know if the potential energy gained by "g_energy -f ener.edr -o" the total potential energy of the system or partial ones like vdw energy. If it is the total energy, to my knowledge it should be negative, and its summation with the kinetic energy should be negative showing the stability of the system. In my simulation, potential energy is positive and the total energy is a big positive number, but no explosion happened. What is the problem? thank you! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] trash error in linux
Hi Mark, I have searched google for sure, but non of the solutions worked out except 'rm' which is a question cleaning remedy rather than solving the main problem! Thanks anyway, Mah On Tue, Jan 6, 2015 at 10:13 AM, mah maz wrote: > Dear all, > > I have encountered a problem much related to linux not Gromacs. I wonder > if anyone has seen this error before : "trash has reached maximum size > please clean manually" while it is actually empty. > any solutions? > > thank you! > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] trash error in linux
Dear all, I have encountered a problem much related to linux not Gromacs. I wonder if anyone has seen this error before : "trash has reached maximum size please clean manually" while it is actually empty. any solutions? thank you! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] atom freezing
Dear Justin, Thank you for your help! Cheers, Mah On Thu, Jan 1, 2015 at 10:07 PM, mah maz wrote: > Thanks Justin! I tried the freezegrps and freezedim but it needed the name > of the groups. As I said in my system only one type of atom is defined. > Should I put the desired atoms in a different group and freeze them? Any > other ways to call the atoms by their numbers? > Regars, > Mah > > On Thu, Jan 1, 2015 at 9:06 PM, mah maz wrote: > >> Dear all, >> >> I want to have different situations for different atoms in my system. In >> the .mdp file how can I freez some of the atoms? ( I dont have residues in >> the system; 3 kinds of atoms are present just by one atom type name) Is it >> possible to assign different situations to some of the atoms by writing >> atom numbers? >> >> thank you! >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] atom freezing
Thanks Justin! I tried the freezegrps and freezedim but it needed the name of the groups. As I said in my system only one type of atom is defined. Should I put the desired atoms in a different group and freeze them? Any other ways to call the atoms by their numbers? Regars, Mah On Thu, Jan 1, 2015 at 9:06 PM, mah maz wrote: > Dear all, > > I want to have different situations for different atoms in my system. In > the .mdp file how can I freez some of the atoms? ( I dont have residues in > the system; 3 kinds of atoms are present just by one atom type name) Is it > possible to assign different situations to some of the atoms by writing > atom numbers? > > thank you! > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] atom freezing
Dear all, I want to have different situations for different atoms in my system. In the .mdp file how can I freez some of the atoms? ( I dont have residues in the system; 3 kinds of atoms are present just by one atom type name) Is it possible to assign different situations to some of the atoms by writing atom numbers? thank you! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] box siz
Hi Justin, Yes, you are right! I think I know what to do now. Thank you very much! Regards, Mah On Wed, Dec 31, 2014 at 12:44 PM, mah maz wrote: > Hi Justin, > > Thank you! > but what are the old and new box? I have defined only one box with > editconf command. > Regards, > Mah > > On Tue, Dec 30, 2014 at 1:58 PM, mah maz wrote: > >> Dear all, >> >> I have calculated the size of the box required for my system. however, >> when applying the g_x2top command with this box size, a fatal error occurs: >> 'couldnt find forcefield for all atoms'. making the box larger in size, >> this error is not appeared. what is the exact problem; box size or >> forcefield? and does the larger box affect the simulation parameters? >> >> Thank you! >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] box siz
Hi Justin, Thank you! but what are the old and new box? I have defined only one box with editconf command. Regards, Mah On Tue, Dec 30, 2014 at 1:58 PM, mah maz wrote: > Dear all, > > I have calculated the size of the box required for my system. however, > when applying the g_x2top command with this box size, a fatal error occurs: > 'couldnt find forcefield for all atoms'. making the box larger in size, > this error is not appeared. what is the exact problem; box size or > forcefield? and does the larger box affect the simulation parameters? > > Thank you! > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] box siz
Dear all, I have calculated the size of the box required for my system. however, when applying the g_x2top command with this box size, a fatal error occurs: 'couldnt find forcefield for all atoms'. making the box larger in size, this error is not appeared. what is the exact problem; box size or forcefield? and does the larger box affect the simulation parameters? Thank you! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] extracting velocities
Hi Tsjerk Got the point. It worked; thanks alot! Regards, Mah On Fri, Dec 26, 2014 at 12:23 PM, mah maz wrote: > Thank you again Tsjerk! You mean -av all_veloc.xvg? Could you please tell > me the differences between -cv veloc.pdb and the mentioned command? > > Regards > ,Mah > > On Fri, Dec 26, 2014 at 10:05 AM, mah maz wrote: > >> Dear all, >> >> What are the ways of extracting velocities from output files? I have used >> g_traj -f traj.trr -s topol.top but couldn't get the velocities. Are there >> any other commands to help me in this regard? >> >> Thank you! >> >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] extracting velocities
Thank you again Tsjerk! You mean -av all_veloc.xvg? Could you please tell me the differences between -cv veloc.pdb and the mentioned command? Regards ,Mah On Fri, Dec 26, 2014 at 10:05 AM, mah maz wrote: > Dear all, > > What are the ways of extracting velocities from output files? I have used > g_traj -f traj.trr -s topol.top but couldn't get the velocities. Are there > any other commands to help me in this regard? > > Thank you! > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] extracting velocities
Dear all, What are the ways of extracting velocities from output files? I have used g_traj -f traj.trr -s topol.top but couldn't get the velocities. Are there any other commands to help me in this regard? Thank you! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] initial velocities
Many thanks Tsjerk and Justin! You both helped alot. Regards, Mah On Wed, Dec 24, 2014 at 10:10 PM, mah maz wrote: > Thank you very much Tsjerk! As far as I know .gro files are coordinate > ones, containing the structure of the system. How is it possible to make > difference between x,y and z AND vx,vy and vz? Should I write the file like > coordinate format? > Regards, > Mah > > On Wed, Dec 24, 2014 at 7:44 PM, mah maz wrote: > >> Dear all, >> >> I want to apply an initial velocity to my system. Is there a possible >> way rather than gen_vel in which I can chose my own wanted velocities? >> And if so, how can I introduce the vx,vy and vz for the atoms? >> >> thank you >> >> >> >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] initial velocities
Thank you very much Tsjerk! As far as I know .gro files are coordinate ones, containing the structure of the system. How is it possible to make difference between x,y and z AND vx,vy and vz? Should I write the file like coordinate format? Regards, Mah On Wed, Dec 24, 2014 at 7:44 PM, mah maz wrote: > Dear all, > > I want to apply an initial velocity to my system. Is there a possible > way rather than gen_vel in which I can chose my own wanted velocities? And > if so, how can I introduce the vx,vy and vz for the atoms? > > thank you > > > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] initial velocities
Dear all, I want to apply an initial velocity to my system. Is there a possible way rather than gen_vel in which I can chose my own wanted velocities? And if so, how can I introduce the vx,vy and vz for the atoms? thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
