Re: [gmx-users] Fwd: Concatenating two trajectories
Hello Venkat, Ya, I am sure that I use 1st.cpt to run next 40 ns job Find below the output of trjcat Summary of files and start times used: FileStart time Time step - complex_prod1_old.xtc0.000 ps 50.000 ps complex_prod1.xtc0.000 ps 50.000 ps WARNING: same Start time as previous Thanks -- View this message in context: http://gromacs.5086.x6.nabble.com/Fwd-Concatenating-two-trajectories-tp5015956p5015962.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Fwd: Concatenating two trajectories
So, that is the problem. Your second trajectory also has the same start time. Some how you didn't extend your second run from where your 1st run has finished. Out of curiosity, why is your time step 50ps? Its too big for a simulation. Generally it should be 2fs. On Mon, Apr 21, 2014 at 12:30 PM, Sunita wrote: > Hello Venkat, > > Ya, I am sure that I use 1st.cpt to run next 40 ns job > Find below the output of trjcat > > Summary of files and start times used: > > FileStart time Time step > - > complex_prod1_old.xtc0.000 ps 50.000 ps > complex_prod1.xtc0.000 ps 50.000 ps WARNING: same > Start time as previous > > Thanks > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Fwd-Concatenating-two-trajectories-tp5015956p5015962.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] System coordinates not getting freezed
You're just trying to measure a potential energy, so do it the right way and don't get involved wiht making mistakes trying to freeze atoms. See http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy Mark On Mon, Apr 21, 2014 at 7:38 AM, sukriti002 wrote: > Hi everyone, > > My system contains one copper ion and one water molecule with no solvent. I > considered complete system as one group and freezed the system. But the > coordinates are not getting fixed. Also when i took the same mdp file with > 2 > copper ions instead of one cu and one water, the system was getting frozen. > Can anyone please let me know what is the problem. > > Regards > Sukriti > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/System-coordinates-not-getting-freezed-tp5015955.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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. > -- 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] Concatenating two trajectories
Dear Sunita Are you sure you have added two trajectory files, one from 0 to 40 and the other from 40 onward ! Because Here *Summary of files and start times used: FileStart time Time step- complex_prod1_old.xtc0.000 ps 50.000 ps complex_prod1.xtc0.000 ps 50.000 ps WARNING: sameStart time as previous* it is saying that you are joining the same two files with same starting time. However, do you have .trr files, GROMACS generally creates .trr files for every successful run. You can try to add those .trr files and later convert them into .xtc files. And you just need to follow like this trjcat -f 1.trr 2.trr -o all.trr That is it. In another case, you said that you are getting strange output in RMSD. Did you check, is there any broken molecule or not ! sometime the broken molecule, due to periodicity, leads to strange RMSD outputs. Thanks Monoj -- 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] Position Restraints with NVT and NPT
The restraints just push on the atoms. If other stuff pushes harder, then the restraints don't work. More relevant is whether you think your starting position models something with accuracy down to a resolution of 0.01nm, or some aspect of the starting position is sensitive to such a difference. (Answer: if it came from an experiment or a simulation, no) Mark On Mon, Apr 21, 2014 at 8:41 AM, zanemarkson wrote: > Thank you Justin! > > I understand usually for regular equilibration, restraints should be > enough. > But I am still wondering to what extent position restraint can restrain my > atoms. In fact, I ran a relatively longer NVT using position restraints and > I saw that both the absolute coordinates of my "restrained" atoms and the > distances between my "restrained" atoms changed by ~0.01nm and I think that > is not negligible any more. I don't know whether this is normal or a > problem > that I should somehow fix. Any thoughts? Thank you! > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Position-Restraints-with-NVT-and-NPT-tp5015953p5015961.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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. > -- 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] Fwd: Concatenating two trajectories
If you want to share a file, please use a file sharing service and share the link. Mark On Mon, Apr 21, 2014 at 7:32 AM, sunita gupta wrote: > Hello Everyone, > > > I have two trajectories of 40 ns each, the first one is from 0 to 40 ns and > next one is extended to next 40 ns taking .cpt file of the first > I concatenating the two using two commands: > 1. trjcat -f 1st.xtc 2nd.xtc -o combine1.xtc -cat > 2. trjcat -f 1st.xtc 2nd.xtc -o combine2.xtc -settime (selecting 0.000 ps > for 1st and 4 ps for 2nd) > > But when I plotted the rmsd using combine1.xtc and combine2.xtc I am > getting very strange plots > > Unfortunately I am not able to post the plots as its saying msg is too big > to be posted and bouncing back... > Can anyone suggest me whats wrong with this method. > > > > > > Best Regards > -- > SUNITA GUPTA > Senior Research Fellow > Bioinformatics Centre > Jawaharlal Nehru University > New Delhi- 110067 > Email- sunita@gmail.com > > > > > > -- > -- > SUNITA GUPTA > Senior Research Fellow > Bioinformatics Centre > Jawaharlal Nehru University > New Delhi- 110067 > Email- sunita@gmail.com > -- > 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. > -- 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] Fwd: Concatenating two trajectories
Hi Venkat, That time step is the time step in the output trajectory. Yours said 2.000 ps, not fs. Cheers, Tsjerk On Apr 21, 2014 9:35 AM, "Venkat Reddy" wrote: > So, that is the problem. Your second trajectory also has the same start > time. Some how you didn't extend your second run from where your 1st run > has finished. > > Out of curiosity, why is your time step 50ps? Its too big for a simulation. > Generally it should be 2fs. > > > On Mon, Apr 21, 2014 at 12:30 PM, Sunita wrote: > > > Hello Venkat, > > > > Ya, I am sure that I use 1st.cpt to run next 40 ns job > > Find below the output of trjcat > > > > Summary of files and start times used: > > > > FileStart time Time step > > - > > complex_prod1_old.xtc0.000 ps 50.000 ps > > complex_prod1.xtc0.000 ps 50.000 ps WARNING: same > > Start time as previous > > > > Thanks > > > > -- > > View this message in context: > > > http://gromacs.5086.x6.nabble.com/Fwd-Concatenating-two-trajectories-tp5015956p5015962.html > > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > > -- > > 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. > > > > > > -- > With Best Wishes > Venkat Reddy Chirasani > PhD student > Laboratory of Computational Biophysics > Department of Biotechnology > IIT Madras > Chennai > INDIA-600036 > -- > 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. > -- 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] Fwd: Concatenating two trajectories
Hi Tsjerk, Sorry for the confusion. I thought its time step which is actually output writing frequency. Thank you sir for the correction. On Mon, Apr 21, 2014 at 2:39 PM, Tsjerk Wassenaar wrote: > Hi Venkat, > > That time step is the time step in the output trajectory. Yours said 2.000 > ps, not fs. > > Cheers, > > Tsjerk > On Apr 21, 2014 9:35 AM, "Venkat Reddy" wrote: > > > So, that is the problem. Your second trajectory also has the same start > > time. Some how you didn't extend your second run from where your 1st run > > has finished. > > > > Out of curiosity, why is your time step 50ps? Its too big for a > simulation. > > Generally it should be 2fs. > > > > > > On Mon, Apr 21, 2014 at 12:30 PM, Sunita wrote: > > > > > Hello Venkat, > > > > > > Ya, I am sure that I use 1st.cpt to run next 40 ns job > > > Find below the output of trjcat > > > > > > Summary of files and start times used: > > > > > > FileStart time Time step > > > - > > > complex_prod1_old.xtc0.000 ps 50.000 ps > > > complex_prod1.xtc0.000 ps 50.000 ps WARNING: same > > > Start time as previous > > > > > > Thanks > > > > > > -- > > > View this message in context: > > > > > > http://gromacs.5086.x6.nabble.com/Fwd-Concatenating-two-trajectories-tp5015956p5015962.html > > > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > > > -- > > > 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. > > > > > > > > > > > -- > > With Best Wishes > > Venkat Reddy Chirasani > > PhD student > > Laboratory of Computational Biophysics > > Department of Biotechnology > > IIT Madras > > Chennai > > INDIA-600036 > > -- > > 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. > > > -- > 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. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] all-angles
Dear Gromacs users I would like to know whether you have ever run a simulation with constraints in "all-angles", or if you know about somebody who did it. When I try to run a protein with this option, it crashes, and only artificial systems like linear chains or modified small molecules seem to work with all-angles. Best regards, Maria -- 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] how to couple a organic molecule in water
Dear gromacs users, I am doing a simulation of an organic molecule in water solution. The organic molecule has 137 atoms (including hydrogen atoms). I have no idea on how to do temperature coupling. I made two temperature groups, one is water, and the other is the organic molecule. I do not know whether it is reasonable. Another way is to couple the organic molecule with the water molecules. Which way is better? Any information on that is appreciated. Best regards Fugui -- 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] g_potential help
Hi All, I have a membrane-protein-solvent system, and I want the potential across the membrane in the direction of the membrane normal. I have 2 questions in that regard. 1) We know that epsilon_r = 80 for the water, ~7 for the membrane-water interface and ~2 for the hydrophobic membrane core. g_potential returns the result for epsilon_r = 1. How can I incorporate this into the result? 2) Default ng =1? Is the number of groups referring to the number of charge groups defined in the topology? Thank you for your time. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Cannot write trajectory frame; maybe you are out of disk space
Dear gromacs users I am doing md simulation on the a protein with 190 residues. I did minimization and equilibration without problem and error. But in production run step (last md simulation with 1500 steps), in step 650, I encountered with following error: File input/output error: Cannot write trajectory frame; maybe you are out of disk space. my mdp file is as follows: - title= opls Protein MD ; Run parameters integrator= md; leap-frog integrator nsteps= 1500; 0.002 * 50 = 1000 ps, 30 ns dt = 0.002; 2 fs ; Output control nstxout= 3000 ; save coordinates every 2 ps nstvout= 3000 ; save velocities every 2 ps nstxtcout= 3000 ; xtc compressed trajectory output every 2 ps nstenergy= 3000 ; save energies every 2 ps nstlog= 3000 ; update log file every 2 ps energygrps = Protein Ion ; Bond parameters continuation= yes; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 10 fs rlist= 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 300 300; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= isotropic; uniform scaling of box vectors tau_p= 2.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= no; Velocity generation is off - If I use df -h command to know disk space, I obtained following information: Filesystem Size Used Avail Use% Mounted on /dev/sda3 220G 14G 196G 7% / none4.0K 0 4.0K 0% /sys/fs/cgroup udev3.0G 4.0K 3.0G 1% /dev tmpfs 607M 1.3M 606M 1% /run none5.0M 0 5.0M 0% /run/lock none3.0G 152K 3.0G 1% /run/shm none100M 64K 100M 1% /run/user /dev/sda6 245G 61G 184G 25% /media/pdfco/my dear /dev/sda2 220G 85G 136G 39% /media/pdfco/Windows /dev/sda5 245G 43G 202G 18% /media/pdfco/nazif -- Is my computer system suitable for this md simulation? How to solve this error? Any help will highly appreciated. -- 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] Cannot write trajectory frame; maybe you are out of disk space
If you can rule out file permissions issues (because you wrote files earlier), and actually running out of disk, usually that would suggest a flaky network file system. Mark On Mon, Apr 21, 2014 at 4:09 PM, Andrew Bostick wrote: > Dear gromacs users > > I am doing md simulation on the a protein with 190 residues. > > I did minimization and equilibration without problem and error. > > But in production run step (last md simulation with 1500 steps), > in step 650, I encountered with following error: > > File input/output error: > Cannot write trajectory frame; maybe you are out of disk space. > > my mdp file is as follows: > > - > title= opls Protein MD > ; Run parameters > integrator= md; leap-frog integrator > nsteps= 1500; 0.002 * 50 = 1000 ps, 30 ns > dt = 0.002; 2 fs > ; Output control > nstxout= 3000 ; save coordinates every 2 ps > nstvout= 3000 ; save velocities every 2 ps > nstxtcout= 3000 ; xtc compressed trajectory output > every 2 ps > nstenergy= 3000 ; save energies every 2 ps > nstlog= 3000 ; update log file every 2 ps > energygrps = Protein Ion > ; Bond parameters > continuation= yes; Restarting after NPT > constraint_algorithm = lincs; holonomic constraints > constraints= all-bonds; all bonds (even heavy atom-H > bonds) constrained > lincs_iter= 1; accuracy of LINCS > lincs_order= 4; also related to accuracy > ; Neighborsearching > ns_type= grid; search neighboring grid cells > nstlist= 5; 10 fs > rlist= 1.0 ; short-range neighborlist cutoff > (in nm) > rcoulomb= 1.0 ; short-range electrostatic cutoff > (in nm) > rvdw= 1.0 ; short-range van der Waals cutoff > (in nm) > ; Electrostatics > coulombtype= PME; Particle Mesh Ewald for > long-range electrostatics > pme_order= 4; cubic interpolation > fourierspacing= 0.16; grid spacing for FFT > ; Temperature coupling is on > tcoupl= V-rescale; modified Berendsen thermostat > tc-grps= Protein Non-Protein; two coupling groups - more > accurate > tau_t= 0.10.1; time constant, in ps > ref_t= 300 300; reference temperature, one for > each group, in K > ; Pressure coupling is on > pcoupl= Parrinello-Rahman; Pressure coupling on in NPT > pcoupltype= isotropic; uniform scaling of box vectors > tau_p= 2.0; time constant, in ps > ref_p= 1.0; reference pressure, in bar > compressibility = 4.5e-5; isothermal compressibility of water, > bar^-1 > ; Periodic boundary conditions > pbc= xyz; 3-D PBC > ; Dispersion correction > DispCorr= EnerPres; account for cut-off vdW scheme > ; Velocity generation > gen_vel= no; Velocity generation is off > > - > > If I use df -h command to know disk space, I obtained following > information: > > Filesystem Size Used Avail Use% Mounted on > /dev/sda3 220G 14G 196G 7% / > none4.0K 0 4.0K 0% /sys/fs/cgroup > udev3.0G 4.0K 3.0G 1% /dev > tmpfs 607M 1.3M 606M 1% /run > none5.0M 0 5.0M 0% /run/lock > none3.0G 152K 3.0G 1% /run/shm > none100M 64K 100M 1% /run/user > /dev/sda6 245G 61G 184G 25% /media/pdfco/my dear > /dev/sda2 220G 85G 136G 39% /media/pdfco/Windows > /dev/sda5 245G 43G 202G 18% /media/pdfco/nazif > > -- > > Is my computer system suitable for this md simulation? > > How to solve this error? > > Any help will highly appreciated. > -- > 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. > -- 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
[gmx-users] Brownian Dynamics
Dear all, I noticed that Gromacs has the option to do Brownian Dynamics, is there anyone who has done that or where can I find any tutorials that can teach me to do it? Thanks. Sincerely Yutian (Shirley) Yang Biomedical and Chemical Engineering 329 Link Hall Syracuse University Syracuse NY 13244 yyan...@syr.edu -- 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] H-bond analysis
Hi, I've never used it myself, hut hbplus allegedly uses a more complex hb criterion. http://www.jhu.edu/fleming/Modeling/HBPLUS.html Kind regards, Erik On 17 Apr 2014, at 10:38, michael.b wrote: > > hi, > > I try to analyze H-bonds in an MD trajectory. > when i look at the definition of an H-bond used by g_hbond it appears > that only three atoms (acceptor, donor, hydrogen, ADH) are used > in the analysis performed by this program ... however, i would assume that > in fact 4 (or up to 6) atoms should be considered because the existence and > the strength of an H-bond not only depend on the A-D distance and > the ADH angle but also on the orientation of the lone pairs of the > acceptor, and the latter are actually determined by the geometry of > the atom(s), call them X, the acceptor is covalently bound to, aren't they? > > So, in short, my question is: is anybody aware of a tool that > can analyze the H-bonds in MD trajectories considering not only > A-D distance and ADH angle but also the position of X (basically > the dihedral DHAX) ? > > thanks for any hints > cheers, > michael > > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/H-bond-analysis-tp5015899.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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. -- 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] negative HB lifetime
Hi, Yes. Or use larger analysis groups if possible. Kind regards, Erik On 17 Apr 2014, at 10:58, Djamila wrote: > Thanks Erik; > You're alright, The problem is in the ACF; it falls dramatically to zero. > In this case, what's the solution? should I extend my simulation to more > time? > Thanks > > Djamila > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/negative-HB-lifetime-tp5015830p5015900.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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. -- 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] How to fix or constrain Center of Mass
Dear Gromacs Users, Is there a way to constrain or fix Center of Mass of lipid bilayer or proteins in a MD run? Thanks! Thomas -- 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] Cannot write trajectory frame; maybe you are out of disk space
Dear Mark Thanks for your reply. I am beginner in linux and gromacs. How to rule out file permissions issues? Which command is true for doing this? Please guide me to solve this problem. -- 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] all-angles
On 4/21/14, 6:21 AM, Maria Astón Serrano wrote: Dear Gromacs users I would like to know whether you have ever run a simulation with constraints in "all-angles", or if you know about somebody who did it. When I try to run a protein with this option, it crashes, and only artificial systems like linear chains or modified small molecules seem to work with all-angles. None of the force fields provided with Gromacs were parametrized with fully rigid angles, so using that option probably just breaks the model physics. I would expect such an option to only be useful for very small molecules that can be sensibly represented as rigid. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Cannot write trajectory frame; maybe you are out of disk space
Did earlier frames get written? Use ls -l, gmxcheck etc. Google about file permissions - unlike on (say) an old Windows machine, on a compute cluster you will not be able to write files anywhere but where you're allowed to. Guessing here, because you haven't supplied any context. Mark On Mon, Apr 21, 2014 at 7:27 PM, Andrew Bostick wrote: > Dear Mark > > Thanks for your reply. > > > I am beginner in linux and gromacs. > > How to rule out file permissions issues? Which command is true for doing > this? > > Please guide me to solve this problem. > -- > 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. > -- 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] how to couple a organic molecule in water
On 4/21/14, 7:53 AM, xiao wrote: Dear gromacs users, I am doing a simulation of an organic molecule in water solution. The organic molecule has 137 atoms (including hydrogen atoms). I have no idea on how to do temperature coupling. I made two temperature groups, one is water, and the other is the organic molecule. I do not know whether it is reasonable. Another way is to couple the organic molecule with the water molecules. Which way is better? Any information on that is appreciated. For a small molecule in water, a single thermostat to the whole system seems to be the most sensible approach to me. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] g_potential help
On 4/21/14, 9:58 AM, rajat desikan wrote: Hi All, I have a membrane-protein-solvent system, and I want the potential across the membrane in the direction of the membrane normal. I have 2 questions in that regard. 1) We know that epsilon_r = 80 for the water, ~7 for the membrane-water interface and ~2 for the hydrophobic membrane core. g_potential returns the result for epsilon_r = 1. How can I incorporate this into the result? I'd venture a guess that the value of epsilon_r in the output is the same as the interpretation of epsilon_r in the .mdp file - it is the relative dielectric permittivity. A value of 1 means don't scale anything; see previous discussions. 2) Default ng =1? Is the number of groups referring to the number of charge groups defined in the topology? No, that means the number of groups you want to analyze, just like g_rdf and other tools sometimes give the option of doing multiple analyses at the same time. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] How to fix or constrain Center of Mass
On 4/21/14, 12:23 PM, Tom wrote: Dear Gromacs Users, Is there a way to constrain or fix Center of Mass of lipid bilayer or proteins in a MD run? To fix the position of the COM, use nstcomm = 1 (but your performance may suffer badly), otherwise removal of COM drift periodically is handled by any value of nstcomm > 0. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] [gmx-developers] Regarding Amber topology and co-ordinate file
Please ask usage questions on the gmx-users mailing list. The development list is for coding and planning discussions; this post is not appropriate here. I am CC'ing this message over to gmx-users. Please post anything further there. On 4/21/14, 10:28 AM, MOHD HOMAIDUR RAHMAN wrote: Dear Gromacs User I have ILs system in small box that is running on Amber 12 MD package. Now I want to use Gromacs MD package for my bigger system (Large no of molecules with proteins) with the same parameter. So, it is possible to convert Amber topology format to gromacs topology format. I have also prep and frcmod file for that molecules. which is use in tleap to generate topology file and Co-ordinate file to direct use in Amber MD package. There are various scripts floating around the web that do such conversions; amb2gmx.pl comes to mind. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Using a forcefield from NAMD
Hi, I am interested in incorporating a nitroxide spin label into my protein simulation. I want to use the Charmm36 force field, and to my knowledge there is no force field for the MTSL spin label in charmm36 for gromacs. What I do have is a charmm22 force field of the MSTL label from NAMD. Is there a way to incorporate this NAMD force field into my gromacs simulations. Best Wishes, Ali Khan -- 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] how to couple a organic molecule in water
Hi Justin, Thank you very much for your information Best regards Fugui At 2014-04-22 01:52:09,"Justin Lemkul" wrote: > > >On 4/21/14, 7:53 AM, xiao wrote: >> Dear gromacs users, >> >> >> I am doing a simulation of an organic molecule in water solution. The >> organic molecule has 137 atoms (including hydrogen atoms). I have no idea on >> how to do temperature coupling. I made two temperature groups, one is water, >> and the other is the organic molecule. I do not know whether it is >> reasonable. Another way is to couple the organic molecule with the water >> molecules. Which way is better? >> Any information on that is appreciated. >> > >For a small molecule in water, a single thermostat to the whole system seems >to >be the most sensible approach to me. > >-Justin > >-- >== > >Justin A. Lemkul, Ph.D. >Ruth L. Kirschstein NRSA Postdoctoral Fellow > >Department of Pharmaceutical Sciences >School of Pharmacy >Health Sciences Facility II, Room 601 >University of Maryland, Baltimore >20 Penn St. >Baltimore, MD 21201 > >jalem...@outerbanks.umaryland.edu | (410) 706-7441 >http://mackerell.umaryland.edu/~jalemkul > >== >-- >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. -- 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] g_potential help
Hi Justin, So different parts of my system in Z-direction should be scaled differently, right? On a coarse level, aqueous part with a scaling of 80, membrane with a scaling of 2? How do I correct for this? Can I take the quantitative output for potential difference across a membrane in water from g_potential literally? Thanks, On Monday, April 21, 2014, Justin Lemkul wrote: > > > On 4/21/14, 9:58 AM, rajat desikan wrote: > >> Hi All, >> >> I have a membrane-protein-solvent system, and I want the potential across >> the membrane in the direction of the membrane normal. I have 2 questions >> in >> that regard. >> >> 1) We know that epsilon_r = 80 for the water, ~7 for the membrane-water >> interface and ~2 for the hydrophobic membrane core. g_potential returns >> the >> result for epsilon_r = 1. How can I incorporate this into the result? >> >> > I'd venture a guess that the value of epsilon_r in the output is the same > as the interpretation of epsilon_r in the .mdp file - it is the relative > dielectric permittivity. A value of 1 means don't scale anything; see > previous discussions. > > 2) Default ng =1? Is the number of groups referring to the number of >> charge >> groups defined in the topology? >> >> > No, that means the number of groups you want to analyze, just like g_rdf > and other tools sometimes give the option of doing multiple analyses at the > same time. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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. > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Using a forcefield from NAMD
On 4/21/14, 3:02 PM, Ali Khan wrote: Hi, I am interested in incorporating a nitroxide spin label into my protein simulation. I want to use the Charmm36 force field, and to my knowledge there is no force field for the MTSL spin label in charmm36 for gromacs. What I do have is a charmm22 force field of the MSTL label from NAMD. Is there a way to incorporate this NAMD force field into my gromacs simulations. You've got parameters in one format, and you need them in another, so all you need to do is convert them. If you've got a stream file that you're reading into NAMD, our Python script should do the job for you. Look for cgenff_charmm2gmx.py: http://mackerell.umaryland.edu/CHARMM_ff_params.html -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] g_potential help
On 4/21/14, 5:11 PM, rajat desikan wrote: Hi Justin, So different parts of my system in Z-direction should be scaled differently, right? On a coarse level, aqueous part with a scaling of 80, membrane with a scaling of 2? How do I correct for this? Can I take the quantitative output for potential difference across a membrane in water from g_potential literally? You don't need to scale anything. The force field parameters for every biomolecular force field that I know of are based on epsilon_r = 1, i.e. no special alteration of vacuum permittivity. The results, at face value, should be sufficient. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] calculation speed of GROMACS and cut off parameters
Hi everyone, I am using GROMACS to simulate bilayers, and I am testing two sets of parameters at present. However, I found significant differences of simulation speed of these two parameters sets. The mainly differences between these parameters are the cut off parameters or of the VDW and coulomb interactions, in the first parameter set, a cut off of 1.0 nm was used for both of the VDW and the coulomb interactions. In the second parameter set, a cut off 1.4 was used for the coulomb interactions, whereas a switch from 1.4 nm to 1.5 nm was used for the VDW parameters. Under the first parameter set, my system could run about 20 ns per day, whereas for the second parameter set, my system only run 7-8 ns per day. So I am wondering if this is only raised because of the cut off parameters? And is this a normal pheonomen? I am listing the mdp file at the end of this email. Please note the only relevarent differences between these two parameter sets are the cut off differences. With my best regards, rxgu the first parameter set: title = NPT Equilibration integrator = md nsteps = 2500 dt = 0.002 nstxout= 0 nstvout= 0 nstenergy = 1000 nstlog = 2000 nstxtcout = 2000 xtc-precision = 1 constraint_algorithm = lincs constraints= all-bonds lincs_iter = 1 lincs_order= 4 ;cutoff-scheme = Verlet ns_type= grid nstlist= 10 rlist = 1.0 coulombtype= PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.0 DispCorr = EnerPres pme_order = 4 fourierspacing = 0.12 optimize_fft = yes pbc= xyz tcoupl = V-rescale tc-grps= POPC SOL tau_t = 0.5 0.5 ref_t = 323 323 pcoupl = Berendsen pcoupltype = semiisotropic tau_p = 10.0 10.0 ref_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 gen_vel = yes gen_temp= 323 gen_seed= 82907543 comm-mode = Linear comm-grps = system the second parameter set: title = NPT Equilibration integrator = md nsteps = 2500 dt = 0.002 nstxout= 0 nstvout= 0 nstenergy = 1000 nstlog = 2000 nstxtcout = 2000 xtc-precision = 1 constraint_algorithm = lincs constraints= all-bonds lincs_iter = 1 lincs_order= 4 ;cutoff-scheme = Verlet ns_type= grid nstlist= 10 rlist = 1.4 rlistlong = 1.7 coulombtype= PME rcoulomb = 1.4 vdwtype = Switch rvdw = 1.5 rvdw-switch= 1.4 DispCorr = EnerPres pme_order = 4 fourierspacing = 0.12 optimize_fft = yes pbc= xyz tcoupl = V-rescale tc-grps
Re: [gmx-users] calculation speed of GROMACS and cut off parameters
On 4/21/14, 5:48 PM, mirc...@sjtu.edu.cn wrote: Hi everyone, I am using GROMACS to simulate bilayers, and I am testing two sets of parameters at present. However, I found significant differences of simulation speed of these two parameters sets. The mainly differences between these parameters are the cut off parameters or of the VDW and coulomb interactions, in the first parameter set, a cut off of 1.0 nm was used for both of the VDW and the coulomb interactions. In the second parameter set, a cut off 1.4 was used for the coulomb interactions, whereas a switch from 1.4 nm to 1.5 nm was used for the VDW parameters. Under the first parameter set, my system could run about 20 ns per day, whereas for the second parameter set, my system only run 7-8 ns per day. So I am wondering if this is only raised because of the cut off parameters? And is this a normal pheonomen? Yes, it's normal. The most important thing to know is you need to use the parameters for which the force field was designed. Lipids are extremely sensitive to changes in the cutoff. Varying these values is very hazardous, so if you're doing something non-standard, you'd better have a lot of good proof that what you're doing isn't going to lead to artifacts. -Justin I am listing the mdp file at the end of this email. Please note the only relevarent differences between these two parameter sets are the cut off differences. With my best regards, rxgu the first parameter set: title = NPT Equilibration integrator = md nsteps = 2500 dt = 0.002 nstxout= 0 nstvout= 0 nstenergy = 1000 nstlog = 2000 nstxtcout = 2000 xtc-precision = 1 constraint_algorithm = lincs constraints= all-bonds lincs_iter = 1 lincs_order= 4 ;cutoff-scheme = Verlet ns_type= grid nstlist= 10 rlist = 1.0 coulombtype= PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.0 DispCorr = EnerPres pme_order = 4 fourierspacing = 0.12 optimize_fft = yes pbc= xyz tcoupl = V-rescale tc-grps= POPC SOL tau_t = 0.5 0.5 ref_t = 323 323 pcoupl = Berendsen pcoupltype = semiisotropic tau_p = 10.0 10.0 ref_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 gen_vel = yes gen_temp= 323 gen_seed= 82907543 comm-mode = Linear comm-grps = system the second parameter set: title = NPT Equilibration integrator = md nsteps = 2500 dt = 0.002 nstxout= 0 nstvout= 0 nstenergy = 1000 nstlog = 2000 nstxtcout = 2000 xtc-precision = 1 constraint_algorithm = lincs constraints= all-bonds lincs_iter = 1 lincs_order= 4 ;cutoff-scheme = Verlet ns_type= grid nstlist= 10 rlist = 1.4 rlistlong = 1.7 coulombtype= PME rcoulomb = 1.4 vdwtype = Switch rvdw = 1.5 rvdw-switch= 1.4 DispCorr = EnerPres pme_order = 4 fourierspacing = 0.12 optimize_fft = yes pbc= xyz tcoupl = V-rescale tc-grps= POPC SOL tau_t = 0.5 0.5 ref_t = 323 323 pcoupl = Berendsen pcoupltype = semiisotropic tau_p = 10.0 10.0 ref_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 gen_vel = yes gen_temp= 323 gen_seed= 82907543 comm-mode = Linear comm-grps = System -- -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] g_potential help
Thank you! On Tuesday, April 22, 2014, Justin Lemkul wrote: > > > On 4/21/14, 5:11 PM, rajat desikan wrote: > >> Hi Justin, >> >> So different parts of my system in Z-direction should be scaled >> differently, right? On a coarse level, aqueous part with a scaling of 80, >> membrane with a scaling of 2? How do I correct for this? Can I take the >> quantitative output for potential difference across a membrane in water >> from g_potential literally? >> >> > You don't need to scale anything. The force field parameters for every > biomolecular force field that I know of are based on epsilon_r = 1, i.e. no > special alteration of vacuum permittivity. The results, at face value, > should be sufficient. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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. > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Cannot write trajectory frame; maybe you are out of disk space
Dear Mark Thanks for your reply. I googled file permission in linux OS. After that I did following steps: I created a directory entitled input. I put pdb and mdp files in the input directory. I used following command to change permission: chmod -R 777 input Now I will md simulation steps (pdb2gmx editconf ..) Is my manner true? -- 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] Fwd: Concatenating two trajectories
Hello Venkat, Yeah, I think by default it will give 0 ps as start time for both trajectories and it should be set by user using -settime flag Correct me if I am wrong. Regards -- View this message in context: http://gromacs.5086.x6.nabble.com/Fwd-Concatenating-two-trajectories-tp5015956p5015992.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] No default U-B types
Hi all, There is an unnatural sidechain in my input file, so I added new lines as new-defined(DPP) residue to the .rtp and .hdb files. Also there were some missed bonds, angles, and dihedrals in generated .top file, which manually added in. When I go through the grompp to do EM, I find a fatal error about the new defined residue: No default U-B types As I checked this kind of angle, it exists in other residues such as lysine as well. This angle is (defined by atom types): CT1 CT2 NH3 I checked the atom names, It seems ok. Part of the top file is as follow: residue 1 DPP rtp DPP q +2.0 1 NH3 1 DPP N 1 -0.3 14.007 ; qtot -0.3 2 HC 1 DPP H1 2 0.33 1.008 ; qtot 0.03 3 HC 1 DPP H2 3 0.33 1.008 ; qtot 0.36 4 HC 1 DPP H3 4 0.33 1.008 ; qtot 0.69 5 CT1 1 DPP CA 5 0.21 12.011 ; qtot 0.9 6 HB 1 DPP HA 6 0.1 1.008 ; qtot 1 7 CT2 1 DPP CB 7 0.21 12.011 ; qtot 1.21 8 HA 1 DPP HB1 8 0.05 1.008 ; qtot 1.26 9 HA 1 DPP HB2 9 0.05 1.008 ; qtot 1.31 10 NH3 1 DPP NG 10 -0.3 14.007 ; qtot 1.01 11 HC 1 DPP HG1 11 0.33 1.008 ; qtot 1.34 12 HC 1 DPP HG2 12 0.33 1.008 ; qtot 1.67 13 HC 1 DPP HG3 13 0.33 1.008 ; qtot 2 14 C 1 DPP C 14 0.51 12.011 ; qtot 2.51 15 O 1 DPP O 15 -0.51 15.999 ; qtot 2 Fatal error: ERROR 1 [file topol.top, line 853]: No default U-B types line 853: 5 7 10 5 Would you please let me your suggestions about the reason of this error? How can I pass it? Would you please help me? Thanks in advance for your suggestions. Sincerely, Shima -- 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.
