[gmx-users] ERROR: invalid enum 'xy' for variable pbc, using 'xyz'
Dear GROMACS Gurus, I am trying to create an infinite sheet of graphene using periodic boundary conditions. I created a sheet which fills the entire xy plane and thought that all I needed to do was put the line pbc=xy into the mdp file. However, when I run the simulation, I get the following error: ERROR: invalid enum 'xy' for variable pbc, using 'xyz' Next time use one of: 'xyz' 'no' 'full' This error confuses me since in the manual it clearly states on page 146, within the Run Parameters and Programs section, that the options for pbc are 'xyz', 'no', or 'xy', which is in contradiction to the error message. Can you please resolve this contradiction for me and let me know if there is something else I need to do in order to get a simulation running with periodic boundary conditions? Thanks. Darrell ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ERROR: invalid enum 'xy' for variable pbc, using 'xyz'
Darrell Koskinen wrote: Dear GROMACS Gurus, I am trying to create an infinite sheet of graphene using periodic boundary conditions. I created a sheet which fills the entire xy plane and thought that all I needed to do was put the line pbc=xy into the mdp file. However, when I run the simulation, I get the following error: ERROR: invalid enum 'xy' for variable pbc, using 'xyz' Next time use one of: 'xyz' 'no' 'full' This error confuses me since in the manual it clearly states on page 146, within the Run Parameters and Programs section, that the options for pbc are 'xyz', 'no', or 'xy', which is in contradiction to the error message. Can you please resolve this contradiction for me and let me know if there is something else I need to do in order to get a simulation running with periodic boundary conditions? pbc=xy is only implemented in GROMACS 4. Are you using an earlier version? (Hint: it's always best to quote your version when asking for help!) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Scaling problems in 8-cores nodes with GROMACS 4.0x
Hi, This problem is not very strange at all. Different CPU's have different efficiencies for different types of code. In this case the Opteron and new Xeon have measurably different (although probably not more than 20%) relative performance for particle-particle and PME interactions. Also, your results tell you exactly what the problem is. If without seperate PME nodes PME takes 44.1% of the time, you will not get good load balancing by using 5 PP and 3 PME nodes (which gives 37.5% PME processing power). You can simply try different -npme, including 0, and see when you get the best performance. BTW, a cut-off of 1.0 nm with a fourierspacing of 0.16 gives pretty bad accuracy, you should increase the cut-off or decrease the spacing. A reasonable ratio off cut-off/fourier_spacing is 8. Increasing the cut-off will reduce the relative PME load, which will make load balancing easier and PME communication less costly. Berk Date: Wed, 2 Sep 2009 21:52:47 -0500 From: dadri...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Scaling problems in 8-cores nodes with GROMACS 4.0x Dear Gromacs users, (all related to GROMACS ver 4.0.x) I am facing a very strange problem on a recently acquired supermicro 8 XEON-cores nodes (2.5GHz quad-core/node, 4G/RAM with the four memory channels activated, XEON E5420, 20Gbs Infiniband Infinihost III Lx DDR): I had been testing these nodes with one of our most familiar protein model (49887 atoms: 2873 for protein and the rest for water into a dodecahedron cell) which I known scales almost linearly until 32 cores in a quad-core/node Opteron 2.4 GHz cluster. Now, with our recently acquired nodes I have severe imbalance PME/PP ratios (from 20% and up). At the beginning I think that this problem was related to Infiniband latency problems, but recently I made a test that gave me a big surprise: since my model scales very well to 8 cores I spreaded it to 8 cores into four machines and the performance was the same than in a single node, which in turns suggests that the problem could be caused by a different reason that latency. After several tests I realized that the problem arises when the process is divided into PME and PP nodes, even into a single node!!!, it is to say: -if for a short job I do (it is exactly the same for a long run): srun -n8 /home/dsilva/PROGRAMAS/gromacs-4.0.5-mavapich2_gcc-1.2p1/bin/mdrun -v -dlb yes -deffnm FULL01/full01 Average load imbalance: 0.7 % Part of the total run time spent waiting due to load imbalance: 0.2 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 % R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-CyclesSeconds % --- Domain decomp. 8101 19.1237.6 2.5 Vsite constr. 8 10012.1890.9 0.3 Comm. coord. 8 10015.8102.3 0.8 Neighbor search8101 51.432 20.4 6.7 Force 8 1001 250.938 99.532.7 Wait + Comm. F 8 1001 15.0646.0 2.0 PME mesh 8 1001 337.946 133.944.1 Vsite spread 8 20022.9911.2 0.4 Write traj.8 20.6040.2 0.1 Update 8 1001 17.8547.1 2.3 Constraints8 1001 35.782 14.2 4.7 Comm. energies 8 10011.4070.6 0.2 Rest 8 25.889 10.3 3.4 --- Total 8 767.030 304.0 100.0 --- Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 38.000 38.000100.0 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance:254.161 14.534 11.380 2.109 which in turns reflects that there are not separation between PME and PP and scaling is almost lineal compared with 1 processor. But if I force PME, and use exactly the same number of processors : srun -n8 --cpu_bind=rank /home/dsilva/PROGRAMAS/gromacs-4.0.5-mavapich2_gcc-1.2p1/bin/mdrun -v -dlb yes -npme 3 -deffnm FULL01/full01 Average load imbalance: 0.5 % Part of the total run time spent waiting due to load imbalance: 0.2 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Average PME mesh/force load: 1.901 Part of the total run time spent waiting due to PP/PME imbalance: 23.9 % NOTE: 23.9 % performance was lost because the PME nodes had more work to do than the PP nodes. You might
Re: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center
Hi Berk, Shorter tau_p? I thought you suggested 5.0 or 10.0 ps ? On Wed, Sep 2, 2009 at 5:28 PM, Berk Hess g...@hotmail.com wrote: Hi, I also just recalled that we have a bug report open since two years already about drift of the COM: http://bugzilla.gromacs.org/show_bug.cgi?id=165 But in that case double precision did not change anything, so that does not seem to be a precision issue. Here tau_p was 1 ps, but up till now we did not manage to find the source of this problem. Thus it would be useful to see if a shorter tau_p fixes it in your case. Berk -- Date: Wed, 2 Sep 2009 17:21:46 +0200 Subject: Re: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center From: mariagorano...@gmail.com To: gmx-users@gromacs.org I will change the tau_p values, and report back. This might take more than a week though. maria On Wed, Sep 2, 2009 at 5:16 PM, Berk Hess g...@hotmail.com wrote: It might actually affect the center of mass motion removal, because you would be scaling your system with 1 +- 1 bit at every step. This could produce consistent rounding in one direction in single precision, causing the system to move in one direction. This is something we should check in general. Often people are using too small tau_p values, like 0.5 or 1 ps, so I advise them to use 5 or 10 ps. But if larger values cause problems in single precision we should be aware of this. Could you report back if changing tau_p solves the drifting problem? Berk -- Date: Wed, 2 Sep 2009 17:06:50 +0200 Subject: Re: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center From: mariagorano...@gmail.com To: gmx-users@gromacs.org Oh dear. That is not good. the missing decimal point in tau_p it is a typo all right. but it seems i have used it in the simulations too. thank you for noticing, Xavier. that forces redoing a lot of simulations. that said, it should still not impact the center of mass removal anyway? -maria On Wed, Sep 2, 2009 at 4:50 PM, XAvier Periole x.peri...@rug.nl wrote: your second value for tau_p is missing the . is this a typo? On Sep 2, 2009, at 4:45 PM, maria goranovic wrote: Here are the mdp parameters: title= POPC cpp = /usr/bin/cpp integrator = md tinit= 0.0 dt = 0.030 nsteps = 300 nstcomm = 1 comm-grps = Lipid W ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 3 nstvout = 3 nstfout = 0 nstlog = 3 nstenergy= 3 ns_type = grid nstlist = 10 pbc = xyz rlist= 1.2 ; Method for doing electrostatics = coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r= 15 vdw_type = Shift ; cut-off lengths= rvdw_switch = 0.9 rvdw = 1.2 DispCorr = No ; Temperature coupling = tcoupl = Berendsen tc-grps = Lipid W tau_t= 0.3 0.3 ref_t= 323 323 ; Pressure coupling = Pcoupl = berendsen Pcoupltype = semiisotropic tau_p = 3.030 compressibility = 3e-53e-5 ref_p = 1.01.0 constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 30 On Wed, Sep 2, 2009 at 4:33 PM, Berk Hess g...@hotmail.com wrote: Hi, I am 99.99% sure that there is no problem with COM motion removal in Gromacs. Could you post your mdp parameters? Berk From: x.peri...@rug.nl To: gmx-users@gromacs.org Subject: Re: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center Date: Wed, 2 Sep 2009 16:04:39 +0200 I am not sure how to fix the trajectory that has drifted ... But if your bilayer drifts even if you use a removal of the COM for the water and bilayer separately that means there is problem in the code! And this should be fixed. XAvier. On Sep 2, 2009, at 3:36 PM, maria goranovic wrote: Dear Experts I had posted this earlier, but the problem was not solved by earlier suggestions. So am posting again. I am simulating a POPC bilayer using MARTINI. The simulation ran fine, but the bilayer drifted towards the edge of the box along the bilayer normal, and eventually some of the atoms crossed the box boundaries. In some cases, entire lipid molecules
RE: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center
I meant 3 instead of 30 ps. I would say 1 ps is too short for systems with a phase with large molecules___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] msd
Hello together, i have a problem with msd. i simulate a melt of chain molecules consisting of 116 united atoms per chain. then i copy the box n times in x,y,z directions, repeat simulations and get a slightly different msd curves: in the time range between 1 ps and 10 ps it flattens out decreasing the curvature for larger boxes and at later time (10ps) follows at higher msd just parallel to the curve for smaller box. the boxe sizes were tried between 3 to 15 Rg's (gyration radii), so if it would be the finite size effect it should already disappear, but it doesnt. I also tried with different thermostats (sd, md with nose-hoover), different tau_t and also switching off the removal of com (then the box starts to fly after awhile) To check from the other side if it could be the finite size effect i reduce the length of the chains from 116 to 58 and the whole msd curve shifted up, also in ballistic regime where one can expect no influence of chain configuration. interesting that the shift is by factor of ~2 (although is not exactly): perhaps i'm just doing sth wrong! msd was calculated for chains using: g_msd -mol diff_mol.xvg is anybody aware of such things or has ideas what was done wrong? Thanks a lot in advance for any suggestions! Regards, Leonid ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GROMACS in Windows Command Prompt
Hi all I use GROMACS 4.0.4 installed on a Windows XP machine through the Cygwin shell. I have just discovered that if I add the variable GROMACS with variable value ...path\GROMACS in the System - Advanced - Environment Variables - User variables section of the control panel and also add the entry ...path\GROMACS\bin (pointing to the GROMACS binaries) at the path line of the system variables section on the same tab, then I can run GROMACS and its utilities through the command prompt. I have not yet checked if the output is the same with the one obtained using the Cygwin shell but at least you have an alternative. I am waiting for your feedback George Tsigaridas___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS in Windows Command Prompt
George Tsigaridas wrote: Hi all I use GROMACS 4.0.4 installed on a Windows XP machine through the Cygwin shell. OK, so *use* the Cygwin shell... there are much easier ways of setting environment variables for the Cygwin shells than through the XP control panel (though, rarely, this can be necessary). Those easier ways are exactly the ones you might need (to learn ) for *nix shells on other systems. I have just discovered that if I add the variable GROMACS with variable value ...path\GROMACS That should do nothing at all. in the System - Advanced - Environment Variables - User variables section of the control panel and also add the entry ...path\GROMACS\bin (pointing to the GROMACS binaries) at the path line of the system variables section on the same tab, then I can run GROMACS and its utilities through the command prompt. Yes, that's what the path variable is for. Much more effective is running a Cygwin shell (the XP command prompt is nowhere near as useful as any Cygwin shell) and following the standard practice here http://oldwiki.gromacs.org/index.php/Installation#Getting_access_to_GROMACS_after_installation I have not yet checked if the output is the same with the one obtained using the Cygwin shell but at least you have an alternative. There's more to GROMACS life than being able to run the executables. Do yourself a favour and try to ignore the fact that you're running on XP as much as possible. You want to learn workflows that are transferable to other environments, not partially-effective XP-specific workflows. Also, to save myself some time in the future, you should avoid using Windows-specific file editing tools unless you know how to take care of line-ending problems yourself with dos2unix. Learn to use vi or emacs from a Cygwin shell. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] msd
Hi, g_msd calculates the msd for molecules, not for atoms. I guess that would explain the result when you half the chain length. It might also explain the box size effects, since whole chains will still have a reduction in MSD due to periodiciy with a box of 3 Rg. If you run g_msd without -mol you get the MSD per atom. Berk From: yel...@uni-mainz.de To: gmx-users@gromacs.org Date: Thu, 3 Sep 2009 15:22:40 +0200 Subject: [gmx-users] msd Hello together, i have a problem with msd. i simulate a melt of chain molecules consisting of 116 united atoms per chain. then i copy the box n times in x,y,z directions, repeat simulations and get a slightly different msd curves: in the time range between 1 ps and 10 ps it flattens out decreasing the curvature for larger boxes and at later time (10ps) follows at higher msd just parallel to the curve for smaller box. the boxe sizes were tried between 3 to 15 Rg's (gyration radii), so if it would be the finite size effect it should already disappear, but it doesnt. I also tried with different thermostats (sd, md with nose-hoover), different tau_t and also switching off the removal of com (then the box starts to fly after awhile) To check from the other side if it could be the finite size effect i reduce the length of the chains from 116 to 58 and the whole msd curve shifted up, also in ballistic regime where one can expect no influence of chain configuration. interesting that the shift is by factor of ~2 (although is not exactly): perhaps i'm just doing sth wrong! msd was calculated for chains using: g_msd -mol diff_mol.xvg is anybody aware of such things or has ideas what was done wrong? Thanks a lot in advance for any suggestions! Regards, Leonid ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS in Windows Command Prompt
OK Mark. But at least, I wonder if the use of the command prompt is going to make easier the application of MPI in a PC network running Windows XP (see also my previous message). What's your opinion? Thanks George - Original Message - From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, September 03, 2009 5:20 PM Subject: Re: [gmx-users] GROMACS in Windows Command Prompt George Tsigaridas wrote: Hi all I use GROMACS 4.0.4 installed on a Windows XP machine through the Cygwin shell. OK, so *use* the Cygwin shell... there are much easier ways of setting environment variables for the Cygwin shells than through the XP control panel (though, rarely, this can be necessary). Those easier ways are exactly the ones you might need (to learn ) for *nix shells on other systems. I have just discovered that if I add the variable GROMACS with variable value ...path\GROMACS That should do nothing at all. in the System - Advanced - Environment Variables - User variables section of the control panel and also add the entry ...path\GROMACS\bin (pointing to the GROMACS binaries) at the path line of the system variables section on the same tab, then I can run GROMACS and its utilities through the command prompt. Yes, that's what the path variable is for. Much more effective is running a Cygwin shell (the XP command prompt is nowhere near as useful as any Cygwin shell) and following the standard practice here http://oldwiki.gromacs.org/index.php/Installation#Getting_access_to_GROMACS_after_installation I have not yet checked if the output is the same with the one obtained using the Cygwin shell but at least you have an alternative. There's more to GROMACS life than being able to run the executables. Do yourself a favour and try to ignore the fact that you're running on XP as much as possible. You want to learn workflows that are transferable to other environments, not partially-effective XP-specific workflows. Also, to save myself some time in the future, you should avoid using Windows-specific file editing tools unless you know how to take care of line-ending problems yourself with dos2unix. Learn to use vi or emacs from a Cygwin shell. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php No virus found in this incoming message. Checked by AVG - www.avg.com Version: 8.5.409 / Virus Database: 270.13.76/2342 - Release Date: 09/02/09 18:03:00 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] t_trxframe speed units
Hey, I tried everything you suggested and a couple more things and still it is not possible to get a reasonable speed for the pulled groups (always way beyond the 0.01nm/ps set in the mdp file and mostly containing some high frequence patttern probably related to pbc). (I tried: constraint, pbcatoms, direction,position and using no ref group). Can I send you a small sample system with the problem or is there something else I can do? Thx, Alex Berk Hess schrieb: But you can not talk about popping back, since there is pbc. What matters is how the pull code determines the distance. At least in 4.0.4 and 4.0.5 it add the rate*t before doing pbc, such that it pulls smoothly even if the distance is larger than the box. But if your force constant is only 1000 it might lag by a lot. Furthermore, if you did not use pull_start, it might start at a random distance with an enormous force. Berk Date: Wed, 2 Sep 2009 15:48:56 +0200 From: alexander.h...@mytum.de To: gmx-users@gromacs.org Subject: Re: [gmx-users] t_trxframe speed units Yes, the diamond moves through the complete sim box (eg. from left to right) before it pops back to the left side due to pbc. But looking at the diamond speed (which is increasing) it looks as if the afm tip is not shifted back to the left side when it leaves the sim box at the right side. If that was the case then the distance of the tip and the group would increase all the time (after the diamond has been shifted back to the left side the first time due to pbc but the afm is not shifted back) which would explain the increasing speed of the diamond. Let me rephrase the question, what happens with the pull position when it reaches the box boundaries?? Is it shifted back (so pull_pos[XX]-=box[XX][XX]) or not? Also, are the atoms shifted back when they leave the box? Berk Hess schrieb: I don't understand what you want to say. The diamond does move a lot right? I think the main problem might be that you use an umbrella potential will an very small force constant (for such large groups). Try using pull=constraint. (and use pull_start=yes) Berk Date: Wed, 2 Sep 2009 15:22:45 +0200 From: alexander.h...@mytum.de To: gmx-users@gromacs.org Subject: Re: [gmx-users] t_trxframe speed units hm.. after thinking about this for a sec I'd say I'm missing an option to apply the pbc to the pull position. Currently it looks as if the position of the afm tip is moving in absolute coordinates further and further away from the original position while the diamonds stay in the original box due to applied pbc. Therefore the distance of the diamond to the afm tip is increasing and hence the force grows bigger and bigger. If I could apply the pbc to the afm position as well then everything would work as expected?? Alex Berk Hess schrieb: Then you were lucky with Gromacs 3. The pull code in Gromacs 3 does not treat pbc at all, so I am surprised that it worked. I just realized that pull_pbcatom is always set in Gromacs 4. Maybe it would be enough to add pull_start=yes. Berk Date: Wed, 2 Sep 2009 14:38:35 +0200 From: alexander.h...@mytum.de To: gmx-users@gromacs.org Subject: Re: [gmx-users] t_trxframe speed units I will try this, thx for the help. Anyways, what is the correct way to do what I want with gromacs 4? (apparently the setup I tryed to use worked for gromacs 3, since I ported the input data from old sims and now I'm trying to recreate the old results). Alex Berk Hess schrieb: The simple issue is that a center of mass is not uniquely defined for a periodic group of particles. If you work on the velocity level, this problem is easy to solve. But the pull code works on the coordinate level. Try with pull_pbcatom set, it might work. Berk Date: Wed, 2 Sep 2009 14:11:11 +0200 From: alexander.h...@mytum.de To: gmx-users@gromacs.org Subject: Re: [gmx-users] t_trxframe speed units We wanted to use 2 slabs so that the net impuls is conserved. Also I'm looking at the slip length, so I actually want to extract the velocity profile of the water in between the two diamond slabs. I'm pulling in x (the pull setup is reproduced at the bottom of the old mail) and I'm using pbc in 3d. What is the problem with pulling the diamond slabs at const speed? I don't actually care where exactly they are. I only care about the boundary condition at the diamond water interface (so that the diamond moves along the surface with v=cst). I mean, I'm pulling with direction not distance, why does direction care about the COM distance?
RE: [gmx-users] t_trxframe speed units
Hi, The only thing I suggested was using pull_start=yes, otherwise you will start at a random distance and you will have enormous forces. Did you try that? Do you have a rectangular or a triclinic box? Berk Date: Thu, 3 Sep 2009 18:00:44 +0200 From: alexander.h...@mytum.de To: gmx-users@gromacs.org Subject: Re: [gmx-users] t_trxframe speed units Hey, I tried everything you suggested and a couple more things and still it is not possible to get a reasonable speed for the pulled groups (always way beyond the 0.01nm/ps set in the mdp file and mostly containing some high frequence patttern probably related to pbc). (I tried: constraint, pbcatoms, direction,position and using no ref group). Can I send you a small sample system with the problem or is there something else I can do? Thx, Alex Berk Hess schrieb: But you can not talk about popping back, since there is pbc. What matters is how the pull code determines the distance. At least in 4.0.4 and 4.0.5 it add the rate*t before doing pbc, such that it pulls smoothly even if the distance is larger than the box___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun running without simulating new steps
Hi Justin, I think it is the minimization issue. I did steep for 2000 steps, and it works thereafter for the mdrun, for this structure. Thank you very much! Regards, Stone Gao -- From: Justin A. Lemkul jalem...@vt.edu Sent: Tuesday, September 01, 2009 4:35 PM To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] mdrun running without simulating new steps st wrote: Hi, I run a two-molecule system with mdrun_d in a water box (~1 water molecules.) The program looks running properly (no errors nor warnnings) However the program seems stop outputting files (because the output file size stop increases) after about 5min. The mdrun_d interface looks normal without any errors, the md.log contains only two saves: snip Grid: 9 x 9 x 14 cells Energies (kJ/mol) Bond Morse Angle G96AngleProper Dih. 3.35232e+053.27635e+017.09937e+021.73811e+01 2.47097e+03 LJ (SR) Coulomb (SR) Coul. recip. PotentialKinetic En. 1.48669e+05 -4.50390e+05 -1.89304e+041.78117e+04 4.38796e+05 Total Energy Conserved En.Temperature Pressure (bar) 4.56608e+054.56608e+051.09892e+03 -5.74950e+04 Step Time Lambda 1000.050000.0 Energies (kJ/mol) Bond Morse Angle G96AngleProper Dih. 3.38536e+051.06967e+032.21584e+044.26526e+01 3.13457e+03 LJ (SR) Coulomb (SR) Coul. recip. PotentialKinetic En. 8.73487e+04 -5.64854e+05 -4.48577e+04 -1.57422e+05 3.56524e+05 Total Energy Conserved En.Temperature Pressure (bar) 1.99102e+057.60608e+058.92881e+027.56563e+04 I'd say the system is exploding. Your temperature is oscillating between 1000 K and 893 K using a Nose-Hoover thermostat, and your potential starts off in excess of 10^4 kJ mol^-1. Did you run any sort of energy minimization or weak-coupling equilibration before this run? It's odd that mdrun wouldn't give some sort of LINCS warning or write out step*.pdb files right beforehand, though. -Justin ** ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g77 error in martini
Dear all, In the martini tutorial there is a approach of martini + ElneDYN . In the tutorial they provided me a script which converts the cleaned pdb structure to CG structure of protein. I compiled the script using g77 (as they recommended) and then I am trying to make the CG structure of 1BL8 protein but it gives me a wierd error Something wrong in the Arg 5. I have no idea how to deal with this error. Do you guys have any idea about this. Your reply for the same will be highly appreciable. Thanks, Sunny ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g77 error in martini
sunny mishra wrote: Dear all, In the martini tutorial there is a approach of martini + ElneDYN . In the tutorial they provided me a script which converts the cleaned pdb structure to CG structure of protein. I compiled the script using g77 (as they recommended) and then I am trying to make the CG structure of 1BL8 protein but it gives me a wierd error Something wrong in the Arg 5. I have no idea how to deal with this error. Do you guys have any idea about this. Your reply for the same will be highly appreciable. Have a look at the original .pdb file. Search for MISSING entries, and you will see that 1BL8 has a substantial number of atoms missing from the structure. One of these is Arg27, which, given the fact that the first 22 residues are missing, becomes Arg5. The first step in any simulation is to understand the flaws in your initial model. In 1BL8, you have to deal with a large amount of missing information. Before doing anything else, you have to model in the missing atoms using the appropriate modeling software. -Justin Thanks, Sunny ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problems with GROMAC/CPMD
Hello all. I have tried to perfomed some simulations about protein dynamics including one copper ion, close from the protein, by Gromacs/CPMD. However, I get some problems during CPMD simulation. In the *.mdp file I added the following: QMMM= yes QMmethod= CPMD QMMMscheme = normal QMMM-grps = QM QMbasis = STO-3G planewavecutoff = 40 qmmmcoul_cutoff = 40 qmbox_cpmd = 40.0 40.0 40.0 ; QM charge QMcharge = 2 ; QM multiplicity QMmult = 1 ; Surface Hopping In the CPMD_inp.tmpl file I added: CPMD INTERFACE GMX MOLECULE CENTER OFF END DFT FUNCTIONAL LDA END SYSTEM SYMMETRY 0 CELL 30.0 1.0 1.0 0.0 0.0 0.0 CUTOFF 110.0 CHARGE 2 END ATOMS *H_VDB.uspp BINARY NEWF TPSEU LMAX=S *C_VDB.uspp BINARY NEWF TPSEU LMAX=P *O_VDB.uspp BINARY NEWF TPSEU LMAX=P *N_VDB.uspp BINARY NEWF TPSEU LMAX=P *Cu_VDB.uspp BINARY NEWF TPSEU LMAX=D LOCAL=P END --- During my simulation I get the above message: * ATOMS NR TYPEX(bohr)Y(bohr)Z(bohr) MBL 1 H 21.823587 25.130608 15.200097 3 2 H 24.280230 24.280222 13.688314 3 3 H 20.236217 24.223539 11.458441 3 4 H 22.082445 21.459965 11.112804 3 5 H 17.140066 21.209700 12.743852 3 6 H 14.522986 19.494656 19.351984 3 7 H 15.663084 23.637722 25.007776 3 8 H 11.751351 25.036116 22.891285 3 9 H 11.789140 23.581034 18.091379 3 10 H 24.969240 15.511571 28.327412 3 11 H 23.656624 18.214203 29.448629 3 12 H 24.922737 20.670853 25.782564 3 13 H 26.491213 18.081922 24.459755 3 14 H 27.596189 19.481304 27.288034 3 15 H 20.372282 15.476724 27.237070 3 16 H 21.691307 22.466095 21.492886 3 17 C 21.011011 22.598375 12.478894 3 18 C 18.800028 21.181072 13.688314 3 19 C 15.058371 21.502331 19.338598 3 20 C 15.133955 22.976320 23.155846 3 21 C 13.111957 23.127495 19.584265 3 22 C 24.091259 17.212650 27.710081 3 23 C 25.924290 18.951195 26.254995 3 24 C 21.483442 16.815811 26.425072 3 25 O 19.102385 20.141733 15.767013 3 26 O 20.840929 18.214203 24.629829 3 27 N 22.692860 23.562132 14.482003 3 28 N 16.683536 22.503889 21.190529 3 29 N 12.998570 23.826700 22.078703 3 30 Cu 21.011011 22.598375 12.478894 3 31 Cu 18.800028 21.181072 13.688314 3 32 Cu 15.058371 21.502331 19.338598 3 33 Cu 15.133955 22.976320 23.155846 3 34 Cu 13.111957 23.127495 19.584265 3 35 Cu 24.091259 17.212650 27.710081 3 36 Cu 25.924290 18.951195 26.254995 3 37 Cu 21.483442 16.815811 26.425072 3 ATOM TYPE= 2 NUM= 1 21.01101110005 22.5983753000112.47889420001 ATOM TYPE= 5 NUM= 1 21.01101110005 22.5983753000112.47889420001 PROGRAM STOPS IN SUBROUTINE SETSYS| ATOMS ARE VERY CLOSE STOP 999 --- I worked only with one copper, but in the CPMD_inp.run file appears multiple copper atoms. Any suggestion about that. Thanks. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem with NPT equilibration
Dear all, I've tried to simulate a membrane system with POPC and protein following Justin's tutorial. The system was minimized with 2 stages. First using restraint on everything accept water for 1 SD steps:- Steepest Descents converged to Fmax 1000 in 1785 steps Potential Energy = -1.69457097061162e+06 Maximum force = 9.15408957613777e+02 on atom 24360 Norm of force = 7.53074616222725e+03 I've proceed with 2nd stage minimization without restraint, Steepest Descents converged to Fmax 1000 in 844 steps Potential Energy = -1.87072963657420e+06 Maximum force = 9.14155621660386e+02 on atom 24360 Norm of force = 7.84646890755063e+03 The energy curve seems ok. With this, i went on with NVT equilibration ( restraint on protein) for 100ps. Both energy and temperature plot look fine also. But it failed while running NPT 1ns(restraint on protein also), it stop with Range checking error, whereby the ci value exceeded the ci cutoff. it is suggested that the minimzation might not done properly. But the minimization were converged in both stages. Is there anything i missed out here? Please advice.Thanks in advance regards bing bing ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Can 3.3.3 and 4.0.5 version exist at the same time?
Hi The 3.3.3 and 4.0.5 version were installed under = * source /usr/gromacs/4.0.5/setup.sh source /usr/gromacs/3.3.3/setup.sh* *The 4.0.5 version is currently the default one.* I want to compare the computation results from 4.0.5 version and 3.3.3 version. So, I write the *source /usr/gromacs/3.3.3/setup.sh* into both my .cshrc file and .pbs file. After this command for 3.3.3 version grompp_mpi -np 16 -v -f minim.mdp -c 6LYZ.gro -p 6LYZ.top -o 6LYZ-EM-vacuum.tpr I obtained the errors shown on the screen. --- Program grompp_mpi, VERSION 4.0.5 Source code file: statutil.c, line: 727 Invalid command line argument: -np --- I Wrapped a Newspaper Round My Head (F. Zappa) What happened? How to solve the problem? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Can 3.3.3 and 4.0.5 version exist at the same time?
Chih-Ying Lin wrote: Hi The 3.3.3 and 4.0.5 version were installed under = * source /usr/gromacs/4.0.5/setup.sh source /usr/gromacs/3.3.3/setup.sh* I've no idea what these scripts are, but the correct procedure is to follow the advice about GMXRC here: http://oldwiki.gromacs.org/index.php/Installation#Getting_access_to_GROMACS_after_installation Now you should be able to source the corresponding file and get everything correctly adjusted for a particular GROMACS version in shell that sourced the file. Alternatively, you could use configure --program-suffix=_xxx and have both available in the same shell, potentially. *The 4.0.5 version is currently the default one.* I want to compare the computation results from 4.0.5 version and 3.3.3 version. So, I write the *source /usr/gromacs/3.3.3/setup.sh* into both my .cshrc file and .pbs file. After this command for 3.3.3 version grompp_mpi -np 16 -v -f minim.mdp -c 6LYZ.gro -p 6LYZ.top -o 6LYZ-EM-vacuum.tpr I obtained the errors shown on the screen. --- Program grompp_mpi, VERSION 4.0.5 Source code file: statutil.c, line: 727 Invalid command line argument: -np --- Clearly the first grompp_mpi in your path is still the 4.0.5 version. If your setup.sh merely appends the 3.3.3 path then your strategy won't work. IIRC, using GMXRC will take care of this issue. Also note that there's no need to compile MPI versions of the tools - configure once with MPI and use make mdrun make install-mdrun, and once without MPI and make make install. In some circumstances, this approach can be essential. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem with NPT equilibration
Bing Bing wrote: Dear all, I've tried to simulate a membrane system with POPC and protein following Justin's tutorial. The system was minimized with 2 stages. First using restraint on everything accept water for 1 SD steps:- Steepest Descents converged to Fmax 1000 in 1785 steps Potential Energy = -1.69457097061162e+06 Maximum force = 9.15408957613777e+02 on atom 24360 Norm of force = 7.53074616222725e+03 I've proceed with 2nd stage minimization without restraint, Steepest Descents converged to Fmax 1000 in 844 steps Potential Energy = -1.87072963657420e+06 Maximum force = 9.14155621660386e+02 on atom 24360 Norm of force = 7.84646890755063e+03 The energy curve seems ok. With this, i went on with NVT equilibration ( restraint on protein) for 100ps. Both energy and temperature plot look fine also. But it failed while running NPT 1ns(restraint on protein also), it stop with Range checking error, whereby the ci value exceeded the ci cutoff. it is suggested that the minimzation might not done properly. But the minimization were converged in both stages. Is there anything i missed out here? That all looks fairly reasonable, but it seems you still need to be more gentle. If the box density differs markedly from the expected value (presumably about 1 g/mL for protein+membrane in water) then the NPT transition will be sharp. You may need to choose a smaller integration step size during the equilibration, or go back and choose a better box size. Obviously, use nstxout=1 and watch where the breakage starts to happen. That may clue you in to a problem. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Bad water sampling ? = A charge group moved too far between two domain decomposition steps ???
Hi The system is one lysozyme + water running on 16 nodes. After = Energy minimization of the solvated systemRelaxation of solvent and hydrogen atom positions: Position restrained MDThen, the error was shown. --- Program mdrun_mpi, VERSION 4.0.5 Source code file: domdec.c, line: 3651 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated --- The energy minimization is as follows ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force 1.0 kJ/mol nsteps = 50; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk But, the above error is still there. My understanding is that A charge group moved too far between two domain decomposition steps comes from the bad water sampling. The bad water sampling will make the charge groups too close. The, they are against each other sharply and leave each other with a high speed. How to solve the problem ?? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Bad water sampling ? = A charge group moved too far between two domain decomposition steps ???
Chih-Ying Lin wrote: Hi The system is one lysozyme + water running on 16 nodes. After = Energy minimization of the solvated systemRelaxation of solvent and hydrogen atom positions: Position restrained MDThen, the error was shown. --- Program mdrun_mpi, VERSION 4.0.5 Source code file: domdec.c, line: 3651 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated --- The energy minimization is as follows ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force 1.0 kJ/mol nsteps = 50; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk But, the above error is still there. My understanding is that A charge group moved too far between two domain decomposition steps comes from the bad water sampling. The bad water sampling will make the charge groups too close. The, they are against each other sharply and leave each other with a high speed. That's possible, but there are other similar hypotheses. I posted some coping strategies earlier today that are also applicable here. If you have a well-formed system, then perhaps you just need to be gentler with it. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Minimisation - particle decomposition
Hi No matter pbc = no or pbc = xyz Energy Minimisation is required with particle decomposition. That is, mdrun -pd is required. Why? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
