Re: [gmx-users] restart md from the point it had stopped
sarbani chattopadhyay wrote: hi, I have been running a molecular dynamics simulation for 2 nanoseconds.But it stopped in the middle because of an internal problem.Is there any way to restart the simulation from the point it has stopped? See http://wiki.gromacs.org/index.php/Doing_Restarts for an expanded discussion. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] No scale up beyond 4 processors for 240000 atom system
Hello, I was wondering what the scale up was with GROMACS 3.3.1 on 8 or 16 processors. Here are my benchmarks: Hardware: Dell PowerEdge 2950, 2x 2,66Ghz Intel Woodcrest CPUs, 8 GB Ram, 2x Gigabit Ethernet GROMACS 3.3.1: 24 atoms, PME, 1.0 nm real cutoff processors ns/day 1 0.141 2 0.253 4 0.409 8 0.232 16 0.107 Do I need to recompile with some other options ? Or is this the best I can get ? Will another type of network improve performance ? It seems communication is the rate limiting step for 8 or 16 cores ? Thank you for the help, -Maria -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Wall Potential
Hi all, I am trying to simulate multiple (2 or 3) tetrapeptides in a cage with Gromacs. However, I would like to constrain the peptides to the centre of the box by enforcing a wall potential in which each of the atoms of the peptide feels a repulsive potential with respect to the edge of the box (or a spherical cage). I am wondering is Gromacs able to perform simulations with such conditions? Any other alternative suggestions with similar functions are greatly appreciated. Many thanks. -- Best regards, Huey Ling ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] No scale up beyond 4 processors for 240000 atom system
From: maria goranovic [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] No scale up beyond 4 processors for 24 atom system Date: Tue, 9 Oct 2007 12:09:50 +0200 Hello, I was wondering what the scale up was with GROMACS 3.3.1 on 8 or 16 processors. Here are my benchmarks: Hardware: Dell PowerEdge 2950, 2x 2,66Ghz Intel Woodcrest CPUs, 8 GB Ram, 2x Gigabit Ethernet GROMACS 3.3.1: 24 atoms, PME, 1.0 nm real cutoff processors ns/day 1 0.141 2 0.253 4 0.409 8 0.232 16 0.107 Do I need to recompile with some other options ? Or is this the best I can get ? Will another type of network improve performance ? It seems communication is the rate limiting step for 8 or 16 cores ? Thank you for the help, -Maria So this is 4 cores sharing one ethernet connection? With such a setup you will never get good scaling. You need something like an Infiniband network. Gromacs 4.0 will give a big improvement, but I don't know how much. Berk. _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] No scale up beyond 4 processors for 240000 atom system
Berk Hess schrieb: Hi all, So this is 4 cores sharing one ethernet connection? perhaps the two Gigabit NICs were bundled somehow. But I guess this doesn't work out-of-the-boxplug'n'play. And latency and not bandwidth may be limiting in this case. With such a setup you will never get good scaling. You need something like an Infiniband network. Or check: Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot and Helmut Grubmuller: Speeding up parallel GROMACS on high-latency networks J. Comp. Chem 28 pp. 2075-2084 (2007) Haven't tried it yet but sounds good! Regards Christian -- Dr. Christian Burisch Lehrstuhl für Biophysik PG Theoretische Biophysik Ruhr-Universität Bochum D-44780 Bochum Raum ND04/67 Fon: +49 234 32 28363 Fax: +49 234 32 14626 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] only one cpu works in my linux cluster
Yeah. Check the machinefile tells mpich what you think it does. It looks pretty certain to be an issue with mpich rather than gromacs. Unfortunately, I don't use mpich any more because I find LAM better. Standard procedure, turn up the verbosity on everything, check the outputs, re-read the relevant manuals. - Original Message From: liu xin [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, October 9, 2007 1:38:50 PM Subject: Re: [gmx-users] only one cpu works in my linux cluster Thanks Alan in fact I've already added the option -machinefile, here's the script: cat $PBS_NODEFILE /home/liuxin/mpd.hosts /home/liuxin/mpich2/bin/mpdboot -n 6 -f mpd.hosts /home/liuxin/mpich2/bin/mpiexec -machinefile $PBS_NODEFILE -np 12 /home/liuxin/ programs/gromacs33mpi/bin/mdrun -v -s 12np.tpr -o -c -e -g -np 12 I am a little busy today, sorry for replying so late... On 10/8/07, Alan Dodd [EMAIL PROTECTED] wrote: Check the MPICH manuals for how to specify the nodes to run on. From memory, the option -machinefile lets you do this. - Original Message From: liu xin [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, October 8, 2007 1:51:12 PM Subject: [gmx-users] only one cpu works in my linux cluster Dear GMXers this is how I've done it so far: grompp -f -c -p -o 12np.tpr -np 12 qsub -l node=6 12np.sh (/home/me/mpich2/bin/mpirun -np 12 mdrun -s 12np.tpr -np 12 ) then it seems my mdrun works fine, but when I ssh to each node to check the cpu efficiency with top, I find that there's only one cpu works with 12 processes! The other nodes are completely idle. the cluster have 56 Intel Xeon duo 3.0G CPUs, below is my system info: Linux login 2.4.21-32.EL #1 SMP Fri Apr 15 21:02:58 EDT 2005 x86_64 x86_64 x86_64 GNU/Linux our administrator have installed mpich1.2.7 in the default DIR (/usr/local), but I have some problems to do mpi-mdrun with mpich1.2.7, so I installed mpich2 in my personal dir. I've searched the list, but cant get any solution. Does it have something to do with the kernel or there's some conflict between mpich1 and 2, or something else? This is the first time I build up a Linux Cluster on my own, ANY suggestions are appreciated ! Xin Liu Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user panel and lay it on us. ___ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Check out the hottest 2008 models today at Yahoo! Autos. http://autos.yahoo.com/new_cars.html___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] only one cpu works in my linux cluster
Thanks for your quick comment Alan :) On 10/9/07, Alan Dodd [EMAIL PROTECTED] wrote: Yeah. Check the machinefile tells mpich what you think it does. It looks pretty certain to be an issue with mpich rather than gromacs. Unfortunately, I don't use mpich any more because I find LAM better. Standard procedure, turn up the verbosity on everything, check the outputs, re-read the relevant manuals. - Original Message From: liu xin [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, October 9, 2007 1:38:50 PM Subject: Re: [gmx-users] only one cpu works in my linux cluster Thanks Alan in fact I've already added the option -machinefile, here's the script: cat $PBS_NODEFILE /home/liuxin/mpd.hosts /home/liuxin/mpich2/bin/mpdboot -n 6 -f mpd.hosts /home/liuxin/mpich2/bin/mpiexec -machinefile $PBS_NODEFILE -np 12 /home/liuxin/ programs/gromacs33mpi/bin/mdrun -v -s 12np.tpr -o -c -e -g -np 12 I am a little busy today, sorry for replying so late... On 10/8/07, Alan Dodd [EMAIL PROTECTED] wrote: Check the MPICH manuals for how to specify the nodes to run on. From memory, the option -machinefile lets you do this. - Original Message From: liu xin [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, October 8, 2007 1:51:12 PM Subject: [gmx-users] only one cpu works in my linux cluster Dear GMXers this is how I've done it so far: grompp -f -c -p -o 12np.tpr -np 12 qsub -l node=6 12np.sh (/home/me/mpich2/bin/mpirun -np 12 mdrun -s 12np.tpr -np 12 ) then it seems my mdrun works fine, but when I ssh to each node to check the cpu efficiency with top, I find that there's only one cpu works with 12 processes! The other nodes are completely idle. the cluster have 56 Intel Xeon duo 3.0G CPUs, below is my system info: Linux login 2.4.21-32.EL #1 SMP Fri Apr 15 21:02:58 EDT 2005 x86_64 x86_64 x86_64 GNU/Linux our administrator have installed mpich1.2.7 in the default DIR (/usr/local), but I have some problems to do mpi-mdrun with mpich1.2.7, so I installed mpich2 in my personal dir. I've searched the list, but cant get any solution. Does it have something to do with the kernel or there's some conflict between mpich1 and 2, or something else? This is the first time I build up a Linux Cluster on my own, ANY suggestions are appreciated ! Xin Liu -- Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user panelhttp://us.rd.yahoo.com/evt=48516/*http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7+and lay it on us. ___ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Pinpoint customers http://us.rd.yahoo.com/evt=48250/*http://searchmarketing.yahoo.com/arp/sponsoredsearch_v9.php?o=US2226cmp=Yahooctv=AprNIs=Ys2=EMb=50who are looking for what you sell. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] limit on energygrp_table
Dear Gromacs users (and developpers) I need to use a force field, derived from ab initio methods, for which the non-bonded interactions between the different atom types is a modified 3-parameters LJ potential. As this kind of potential is not implemented within Gromacs I am using fully tabulated user defined potentials V_i_j for the non bonded interactions between atom types i and j. The problem is that I have many different atomtypes (on the order of 20) and therefore I have to input many groups in the energygrp_table field of my mdp file. When I run grompp I have a message saying that there is a limit on the (254 if I remember correctly) on the number of groups that I can have in the energygrp_table field. -Is there a way to increase this limit (by changing a constant and then recompile) ? or is it more complicated (from the value 254 one could guess that there is some one one-byte optimization) -If the above solution is not an option, is there a simple way to modify the Gromacs source code to use these more advanced potentials while keeping good performances. -Any other suggestion? Thank you for your help. Adrien. -- Adrien Leygue Department of Materials Science and Engineering School of Chemical Engineering National Technical University of Athens 9 Heroon Polytechniou Street Zografou Campus, Athens 157 80, GREECE Tel/Fax: +30210 772-3112 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] limit on energygrp_table
From: Adrien Leygue [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] limit on energygrp_table Date: Tue, 9 Oct 2007 18:13:21 +0300 Dear Gromacs users (and developpers) I need to use a force field, derived from ab initio methods, for which the non-bonded interactions between the different atom types is a modified 3-parameters LJ potential. As this kind of potential is not implemented within Gromacs I am using fully tabulated user defined potentials V_i_j for the non bonded interactions between atom types i and j. The problem is that I have many different atomtypes (on the order of 20) and therefore I have to input many groups in the energygrp_table field of my mdp file. When I run grompp I have a message saying that there is a limit on the (254 if I remember correctly) on the number of groups that I can have in the energygrp_table field. -Is there a way to increase this limit (by changing a constant and then recompile) ? or is it more complicated (from the value 254 one could guess that there is some one one-byte optimization) This is indeed a on-byte optimization. The group numbers are stored as uchars (include/types/atoms.h). You could change this, then you also have to change 2 or more other files for the io and communication of these numbers. -If the above solution is not an option, is there a simple way to modify the Gromacs source code to use these more advanced potentials while keeping good performances. This depends on what combination rules you have for your parameters. If you are lucky, you can use the buckingham 3-parameter setup and modify the plain C buckingham innerloops to calculate your functional form. Berk. _ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] solubility of PVME in TIP5P
Did you noticed that the number of TIP5P water molecules is about half of what's needed to fill the box. I think that's why your box collapsed. JW On 4/23/07, kitty ji [EMAIL PROTECTED] wrote: Dear GMX user, Explicated model of Poly (vinyl methyl ether) was built with ether parameters in OPLS Force Field. The density and radius of gyration of PVME melts fit experimental value well. And then it was solvated in Tip5p. In experiment, PVME should solvate in water well in ~300k. However, it totally collapsed in my model. I have changed temperature and electricity but no help. How can I find a acceptable model? Any suggestion will be appreciated !! I feel increasing the polarity of PVME maybe helpful. Is it right? Thanks in advance. * Ji Qing Polymer Physics Institute of Chemistry, Chinese Academy of Sciences Tel: 0086-10-62562894 ，82618423 * ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Jianwen A Feng Center for Computational Biology Washington University in St. Louis ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] simulating Hexadecane in water
Hello, I'm very new to Gromacs, and I am interested in simulating the interactions of 2 hexadecane (C16H34) molecules in water (SPC/E specificall). I've spent some time experimenting with tutorials in Gromacs, but I've found little help in non-protein simulations like this one. I have built topologies for hexadecane compatible with NAMD, so I figure I should be able to do the same in Gromacs but I'm fuzzy on how to go about doing so. I also don't know what forcefield I should be using for this sort of system. I'd greatly appreciate it if someone could give me some pointers on how to get started here. Thanks very much, Adam ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] 3.3.2 Error when using the mpi option
Hi, I am trying to compile version 3.3.2 in the parallel mode. I use the following options to configure: ./configure --prefix=dir --disable-float -enable-mpi and receive the following error message: checking size of int... configure: error: cannot compute sizeof (int) Note: The non parallel version compiles without errors. Any help? Luciano Dr. Luciano Triguero College of Art and Science Department of Physics and Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] restart md from the point it had stopped
[Tsjerk] why do you write velocities and forces every 10 ps? Third world country my friend, energy supply is not that stable over here. Also the queue to run a process is huuuge, so every hour is important. In the end I do a trjconv to reduce # of frames. Great Doing Restarts whoever wrote it :D http://wiki.gromacs.org/index.php/Doing_Restarts On 10/9/07, Mark Abraham [EMAIL PROTECTED] wrote: sarbani chattopadhyay wrote: hi, I have been running a molecular dynamics simulation for 2 nanoseconds.But it stopped in the middle because of an internal problem.Is there any way to restart the simulation from the point it has stopped? See http://wiki.gromacs.org/index.php/Doing_Restarts for an expanded discussion. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] 3.3.2 Error when using the mpi option
Hi, On Oct 9, 2007, at 6:21 PM, Triguero, Luciano O wrote: Hi, I am trying to compile version 3.3.2 in the parallel mode. I use the following options to configure: ./configure --prefix=dir --disable-float -enable-mpi and receive the following error message: checking size of int... configure: error: cannot compute sizeof (int) Note: The non parallel version compiles without errors. Any help? Luciano Well, even if you probably don't appreciate it right now it's a very good thing (TM). Gromacs tries to use your default MPI compilers (typically mpicc, but you can set it in the variable MPICC), but for some reason it isn't even possible to compile a small program to check the size of an integer. Check config.log and try to find out what's wrong with your MPI- enabled compiler. Cheers, Erik ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] grompp error
hi... i have been trying to do grompp for the following file but am getting this error: There were 1 error(s) processing your inputWARNING 3 [file popc.top, line 32]: 7380 non-matching atom names atom names from popc.top will be used atom names from popc.pdb will be ignored Your topology is incorrect. I am hesitant to assist more because 1) you didn't include your topology here, 2) there is a massive amount of questions exactly like this one for lipid topology problems, and 3) you do not appear to be helping yourself (see next section). double-checking input for internal consistency...ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist.There were 3 warnings This means exactly what it says. Did you read this carefully? your rcoulomb=1.4 therefore your box needs to be longer than 2.8nm, but this error message is telling you that it is not. Therefore make your box bigger. Try this: editconf -f popc.pdb -o popc.gro tail -1 popc.gro -- here you see your box dimensions. WARNING: don't make your box 2.8001nm since it will likely shrink a little if you are doing constant pressure. WARNING: did you even turn on constant pressure? I think not. However you have set some variables for constant pressure ... this is not the same as turning it on. Look at the mdp options for pressure coupling. WARNING: Once you change your box size (the source of the error) then grompp is going to allow you to continue past the warnings (the atom names don't match). If your topology is still incorrect then your next error will be about a 1-4 interaction that is larger than 1nm. But that won't actually be the source of the problem... the source of the problem is that your topology is incorrect. SUGGESTION: make a simple test system with one lipid and one water and no PBC. If you can go through grompp and a short mdrun then you can have some measure of faith in your topology. Chris. The grompp command i am using is: grompp -f 7eq_w.mdp -c popc.pdb -p popc.top -o poc.tpr the inputs are: popc.mdp title= popc128aintegrator = mddefine = -DPOSRES -DFLEX_SPCdt = 0.002nsteps = 25000nstxout = 500ns_type = gridpbc = xyzconstraints = hbondsconstraints_algorithm= shakecoulombtype = PMEvdwtype = cut-offrcoloumb = 1.4 Tcoupl = berendsenpcoupl = berendsentau_t= 0.1 0.1tc_grps = POPC SOLref_t= 300 300ref_p = 1.0pcoupltype = isotropiccompressibility = 4.5e-5gen_temp = 300 popc.top #include ffgmx.itp#include lipid.itp#include popc.itp #ifdef FLEX_SPC#include flexspc.itp#else#include spc.itp#endif #ifdef POSRES_WATER; Position restraint for each water oxygen[ position_restraints ]; i funct fcxfcyfcz 1 1 1000 1000 1000#endif ; Include generic topology for ions#include ions.itp #ifdef POSRES#include lipid_posre.itp#endif [ system ]; NamePure DPPC bilayer with 128 lipids and 3655 water molecules [ molecules ]; Compound#molsPOPC 128SOL 2460 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] No scale up beyond 4 processors for 240000 atom system
Low cost tip: Ask your cluster administrator if it is possible apply channel bonding to the Gigabit interfaces. You need two network switches for that to be efficient (a cut-through switch may also help). It increases network bandwidth by 70%. It also helps to use Cat6 cables. You may try this MPICH compilation: ./configure --with-device=ch3:nemesis --enable-fast --disable-cxx --enable-error-checking=no CFLAGS=-O3 FFLAGS=-O3 There is patch to run PME faster over ethernet... maybe that paper from Dr. Carsten that Dr. Christian suggested. High cost tip: Migrate to Infiniband. Anyone tried GotoBLAS ? Does it work well with GMX ? On 10/9/07, Christian Burisch [EMAIL PROTECTED] wrote: Berk Hess schrieb: Hi all, So this is 4 cores sharing one ethernet connection? perhaps the two Gigabit NICs were bundled somehow. But I guess this doesn't work out-of-the-boxplug'n'play. And latency and not bandwidth may be limiting in this case. With such a setup you will never get good scaling. You need something like an Infiniband network. Or check: Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot and Helmut Grubmuller: Speeding up parallel GROMACS on high-latency networks J. Comp. Chem 28 pp. 2075-2084 (2007) Haven't tried it yet but sounds good! Regards Christian -- Dr. Christian Burisch Lehrstuhl für Biophysik PG Theoretische Biophysik Ruhr-Universität Bochum D-44780 Bochum Raum ND04/67 Fon: +49 234 32 28363 Fax: +49 234 32 14626 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] grompp error
ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. try to Increase the box size or decrease rlist. = as ERROR message suggests Yes, technically you could decrease rlist (rcoulomb actually in this case), but in that case make sure that you know what you are getting into. I would advise against that unless you are sure that you understand the implications. I think that this is a particularly dangerous error message and should be modified in future gromacs distributions. PS, I see that you actually do have the line: pcoupl = berendsen which I had not seen previously when I said: WARNING: did you even turn on constant pressure? I think not. However you have set some variables for constant pressure ... this is not the same as turning it on. Look at the mdp options for pressure coupling. So I was incorrect there. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Criteria and Energy Conservation
Dear GROMACS Users, I'm trying to use GROMACS to get some MD snapshots for single-point quantum mechanical calculations, trying to observe HOMO-LUMO gap of a protein immersed in water with counterions, at a given salt concentration (4600 atoms in total). I'd like to know if they are reliable enough to send to QM calculations. I've got two questions: Which are the criteria I should be looking at? And one of them I've analyzed was energy conservation (I'm doing 300K NVT MD, with 10A cutoff for vdw and coulomb, with PME electrostatics, and double precision), and the manual says a Ekin RMSD/Tot Energy RMSD ratio below 0.05 is fine, but I've got 0.3-0.5 in all simulations I've done. What should I do? Thanks in advance, Gustavo Troiano Feliciano This message was sent using IFUSP Webmail - USP/Sao Paulo/Brazil. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: 3.3.2 trjconv -ur compact -pbc whole problem
GMX users, In 3.3.1, I used trjconv -ur compact -pbc whole to convert a rhombic dodecahedron box so it could be displayed properly in VMD. This does not appear to be working in 3.3.2. Is there another way to convert a box so it displays properly in a visualization program? This is the command that I used, echo 0 | trjconv -ur compact -pbc whole -f 1fsv_heat300.gro -s 1fsv_heat300.gro -o 1fsv_heat300_visual.gro Thanks, JW -- Jianwen A Feng Center for Computational Biology Washington University in St. Louis ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to change the box size during simuation
Hey, Now I'm simulating infinite molecules. I want to change the box size a lit bit every time step so as to induce some stress in this system. Is there any way in gromacs to do this, apart from modifying the code? Thanks in advance. Yours Sincerely, WU Yanbin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: 3.3.2 trjconv -ur compact -pbc whole problem
Using trjconv -ur compact -pbc atom worked. JW On 10/9/07, JW Feng [EMAIL PROTECTED] wrote: GMX users, In 3.3.1, I used trjconv -ur compact -pbc whole to convert a rhombic dodecahedron box so it could be displayed properly in VMD. This does not appear to be working in 3.3.2. Is there another way to convert a box so it displays properly in a visualization program? This is the command that I used, echo 0 | trjconv -ur compact -pbc whole -f 1fsv_heat300.gro -s 1fsv_heat300.gro -o 1fsv_heat300_visual.gro Thanks, JW -- Jianwen A Feng Center for Computational Biology Washington University in St. Louis -- Jianwen A Feng Center for Computational Biology Washington University in St. Louis ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fatal error: Atom CA not found in residue LYSH200 while adding hydrogens
Hi, I have a problem using Gromacs. When I use the pdb2gmx command to generate the .top and .gro files, I got the error: :-) G R O M A C S (-: Gyas ROwers Mature At Cryogenic Speed :-) VERSION 3.3.2 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2007, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) pdb2gmx (-: Option Filename Type Description -f 2FDG.pdb InputGeneric structure: gro g96 pdb tpr tpb tpa xml -o 2FDG.gro Output Generic structure: gro g96 pdb xml -p 2FDG.top Output Topology file -i posre.itp Output Include file for topology -n clean.ndx Output, Opt. Index file -q clean.pdb Output, Opt. Generic structure: gro g96 pdb xml Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint0 Set the nicelevel -[no]merge bool no Merge chains into one molecule definition -ff string select Force field, interactive by default. Use - h for information. -water enum spc Water model to use: with GROMOS we recommend SPC, with OPLS, TIP4P: spc, spce, tip3p, tip4p, tip5p or f3c -[no]inter bool no Set the next 6 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool no Interactive termini selection, iso charged -[no]lys bool no Interactive Lysine selection, iso charged -[no]arg bool no Interactive Arganine selection, iso charged -[no]asp bool no Interactive Aspartic Acid selection, iso charged -[no]glu bool no Interactive Glutamic Acid selection, iso charged -[no]gln bool no Interactive Glutamine selection, iso neutral -[no]his bool no Interactive Histidine selection, iso checking H-bonds -angle real 135 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) -distreal 0.3 Maximum donor-acceptor distance for a H- bond (nm) -[no]una bool no Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine -[no]ignhbool no Ignore hydrogen atoms that are in the pdb file -[no]missing bool no Continue when atoms are missing, dangerous -[no]v bool no Be slightly more verbose in messages -posrefc real 1000Force constant for position restraints -vsite enum noneConvert atoms to virtual sites: none, hydrogens or aromatics -[no]heavyh bool no Make hydrogen atoms heavy -[no]deuterate bool no Change the mass of hydrogens to 2 amu Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 7: Encad all-atom force field, using scaled-down vacuum charges 8: Encad all-atom force field, using full solvent charges 0 Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.rtp Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Reading 2FDG.pdb... WARNING: all CONECT records are ignored Read 'ALKYLATED DNA REPAIR PROTEIN ALKB; 5'-D(P*TP*(MA7)P*T)-3'', 1747 atoms Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file Gave chain 3 chain identifier 'C' There are 3 chains and 1 blocks of water and 324 residues with 1747 atoms chain #res #atoms 1 'A' 200 1556 2 'B' 3 63 3 'C' 2 9 4 '-' 119119 (only water) All occupancies are one Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.atp Atomtype 50 Reading residue
Re: [gmx-users] Fatal error: Atom CA not found in residue LYSH200 while adding hydrogens
Haining, Did you check the structure for missing atoms/residues (REMARK 465/470)? Tsjerk On 10/10/07, Haining Liu [EMAIL PROTECTED] wrote: Hi, I have a problem using Gromacs. When I use the pdb2gmx command to generate the .top and .gro files, I got the error: :-) G R O M A C S (-: Gyas ROwers Mature At Cryogenic Speed :-) VERSION 3.3.2 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2007, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) pdb2gmx (-: Option Filename Type Description -f 2FDG.pdb InputGeneric structure: gro g96 pdb tpr tpb tpa xml -o 2FDG.gro Output Generic structure: gro g96 pdb xml -p 2FDG.top Output Topology file -i posre.itp Output Include file for topology -n clean.ndx Output, Opt. Index file -q clean.pdb Output, Opt. Generic structure: gro g96 pdb xml Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint0 Set the nicelevel -[no]merge bool no Merge chains into one molecule definition -ff string select Force field, interactive by default. Use - h for information. -water enum spc Water model to use: with GROMOS we recommend SPC, with OPLS, TIP4P: spc, spce, tip3p, tip4p, tip5p or f3c -[no]inter bool no Set the next 6 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool no Interactive termini selection, iso charged -[no]lys bool no Interactive Lysine selection, iso charged -[no]arg bool no Interactive Arganine selection, iso charged -[no]asp bool no Interactive Aspartic Acid selection, iso charged -[no]glu bool no Interactive Glutamic Acid selection, iso charged -[no]gln bool no Interactive Glutamine selection, iso neutral -[no]his bool no Interactive Histidine selection, iso checking H-bonds -angle real 135 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) -distreal 0.3 Maximum donor-acceptor distance for a H- bond (nm) -[no]una bool no Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine -[no]ignhbool no Ignore hydrogen atoms that are in the pdb file -[no]missing bool no Continue when atoms are missing, dangerous -[no]v bool no Be slightly more verbose in messages -posrefc real 1000Force constant for position restraints -vsite enum noneConvert atoms to virtual sites: none, hydrogens or aromatics -[no]heavyh bool no Make hydrogen atoms heavy -[no]deuterate bool no Change the mass of hydrogens to 2 amu Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 7: Encad all-atom force field, using scaled-down vacuum charges 8: Encad all-atom force field, using full solvent charges 0 Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.rtp Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Reading 2FDG.pdb... WARNING: all CONECT records are ignored Read 'ALKYLATED DNA REPAIR PROTEIN ALKB; 5'-D(P*TP*(MA7)P*T)-3'', 1747 atoms Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file Gave chain 3 chain identifier 'C' There are 3 chains and 1 blocks of water and 324 residues with 1747 atoms chain #res #atoms 1
Re: [gmx-users] Fatal error: Atom CA not found in residue LYSH200 while adding hydrogens
Tsjerk,I just started to learn Gromacs. But how do I check the missing atoms?Thanks,HainingOn Wed, 10 Oct 2007 06:41:31 +0200 Tsjerk Wassenaar <[EMAIL PROTECTED] />wrote: Haining, Did you check the structure for missing atoms/residues (REMARK 465/470)? Tsjerk On 10/10/07, Haining Liu <[EMAIL PROTECTED] />wrote: Hi, I have a problem using Gromacs. When I use the pdb2gmx command to generate the .top and .gro files, I got the error: :-) G R O M A C S (-: Gyas ROwers Mature At Cryogenic Speed :-) VERSION 3.3.2 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, U! niversity of Groningen, The Netherlands. Copyright (c) 2001-2007, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) pdb2gmx (-: Option Filename Type Description -f 2FDG.pdb Input Generic structure: gro g96 pdb tpr tpb tpa xml -o 2FDG.gro Output Generic structure: gro g96 pdb xml -p 2FDG.top Output Topology file -i posre.itp Output Include fil! e for topology -n clean.ndx Output, Opt. Index file -q clean.pdb Output, Opt. Generic structure: gro g96 pdb xml Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -nice int 0 Set the nicelevel -[no]merge bool no Merge chains into one molecule definition -ff string select Force field, interactive by default. Use - h for information. -water enum spc Water model to use: with GROMOS we recommend SPC, with OPLS, TIP4P: spc, spce, tip3p, tip4p, tip5p or f3c -[no]inter bool no Set the next 6 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool no Interac! tive termini selection, iso charged -[no]lys bool no Interactive Lysine selection, iso charged -[no]arg bool no Interactive Arganine selection, iso charged -[no]asp bool no Interactive Aspartic Acid selection, iso charged -[no]glu bool no Interactive Glutamic Acid selection, iso charged -[no]gln bool no Interactive Glutamine selection, iso neutral -[no]his bool no Interactive Histidine selection, iso checking H-bonds -angle real 135 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) -dist real 0.3 Maximum donor-acceptor distance for a H- bond (nm) -[no]una bool no Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine -[no]ignh bool no Ignore hydrogen! atoms that are in the pdb file -[no]m issing bool no Continue when atoms are missing, dangerous -[no]v bool no Be slightly more verbose in messages -posrefc real 1000 Force constant for position restraints -vsite enum none Convert atoms to virtual sites: none, hydrogens or aromatics -[no]heavyh bool no Make hydrogen atoms heavy -[no]deuterate bool no Change the mass of hydrogens to 2 amu Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vo! l 25 pag 1656) 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 7: Encad all-atom force field, using scaled-down vacuum charges 8: Encad all-atom force field, using full solvent charges 0 Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.rtp Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Reading 2FDG.pdb... WARNING: all CONECT records are ignored Read 'ALKYLATED DNA REPAIR PROTEIN ALKB; 5'-D(P*TP*(MA7)P*T)-3'', 1747 atoms Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file Gave chain 3 chain identifier 'C' There are 3 chains and 1 blocks of water and 324 residues with 1747 atoms! chain #res #atoms 1 ' A' 200 1556 2 'B' 3 63 3 'C' 2 9 4 '-' 119 119 (only water) All occupancies are one Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.atp Atomtype 50 Reading residue database... (ffG43a1) Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.rtp Residue 96 Sorting it all out... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.hdb Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1-n.tdb Opening library file
Re: [gmx-users] Fatal error: Atom CA not found in residue LYSH200 while adding hydrogens
Hi Haining, This has nothing to do with gromacs. The information is in the .pdb file (use a text viewer/editor). Before starting any simulation, you have to know what you're intending to simulate. The model, the .pdb file of it. How the structure was solved, etc., etc. The paper should also state which parts of the molecule were not (well) resolved. In case you have missing atoms and residues, you have to find a way to deal with that (model them in, for example). Did you run the tutorials mentioned on the Gromacs site? Tsjerk On 10/10/07, Haining Liu [EMAIL PROTECTED] wrote: Tsjerk, I just started to learn Gromacs. But how do I check the missing atoms? Thanks, Haining On Wed, 10 Oct 2007 06:41:31 +0200 Tsjerk Wassenaar wrote: Haining, Did you check the structure for missing atoms/residues (REMARK 465/470)? Tsjerk On 10/10/07, Haining Liu wrote: Hi, I have a problem using Gromacs. When I use the pdb2gmx command to generate the .top and .gro files, I got the error: :-) G R O M A C S (-: Gyas ROwers Mature At Cryogenic Speed :-) VERSION 3.3.2 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, U! niversity of Groningen, The Netherlands. Copyright (c) 2001-2007, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) pdb2gmx (-: Option Filename Type Description -f 2FDG.pdb Input Generic structure: gro g96 pdb tpr tpb tpa xml -o 2FDG.gro Output Generic structure: gro g96 pdb xml -p 2FDG.top Output Topology file -i posre.itp Output Include fil! e for topology -n clean.ndx Output, Opt. Index file * -q clean.pdb Output, Opt. Generic structure: gro g96 pdb xml Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -nice int 0 Set the nicelevel -[no]merge bool no Merge chains into one molecule definition -ff string select Force field, interactive by default. Use - h for information. -water enum spc Water model to use: with GROMOS we recommend SPC, with OPLS, TIP4P: spc, spce, tip3p, tip4p, tip5p or f3c -[no]inter bool no Set the next 6 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool no Interac! tive termini selection, iso charged -[no]lys bool no Interactive Lysine selection, iso charged -[no]arg bool no Interactive Arganine selection, iso charged -[no]asp bool no Interactive Aspartic Acid selection, iso charged -[no]glu bool no Interactive Glutamic Acid selection, iso charged -[no]gln bool no Interactive Glutamine selection, iso neutral -[no]his bool no Interactive Histidine selection, iso checking H-bonds -angle real 135 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) -dist real 0.3 Maximum donor-acceptor distance for a H- bond (nm) -[no]una bool no Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine -[no]ignh bool no Ignore hydrogen! atoms that are in the pdb file -[no]m issing bool no Continue when atoms are missing, dangerous -[no]v bool no Be slightly more verbose in messages -posrefc real 1000 Force constant for position restraints -vsite enum none Convert atoms to virtual sites: none, hydrogens or aromatics -[no]heavyh bool no Make hydrogen atoms heavy -[no]deuterate bool no Change the mass of hydrogens to 2 amu Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vo! l 25 pag 1656) * * 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 7: Encad all-atom force field, using scaled-down vacuum charges 8: Encad all-atom force field, using full solvent charges 0 Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.rtp Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Reading 2FDG.pdb... WARNING: all CONECT records are ignored Read 'ALKYLATED DNA REPAIR PROTEIN ALKB; 5'-D(P*TP*(MA7)P*T)-3'', 1747 atoms Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing
[gmx-users] anisotropic pressure coupling for temperature annealing
Dear gmx-users, I used anisotropic p-coupling for lipid bilayers and annealed the system from 330K-300K at the ratio of 2 degree/ns.And the x dimension and y dimension increased with time in the whole procedure, but actually the area/lipid should decrease when tempreture decreases. I think there may due to the P couple parameters I used. Now I write them here: tau_p = 2.0 2.0 2.0 0 0 0 compressibility = 4.5e-6 4.5e-6 4.5e-6 0 0 0 ref_p = 11 1 1 1 1 Is there anything wrong with my parameter? or should I use ref_p = 11 1 0 0 0 I saw someone use this ref_p before. Any suggestion will be appreciated, thanks in advance. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] anisotropic pressure coupling for temperature annealing
Q733 wrote: Dear gmx-users, I used anisotropic p-coupling for lipid bilayers and annealed the system from 330K-300K at the ratio of 2 degree/ns.And the x dimension and y dimension increased with time in the whole procedure, but actually the area/lipid should decrease when tempreture decreases. I think there may due to the P couple parameters I used. Now I write them here: tau_p = 2.0 2.0 2.0 0 0 0 compressibility = 4.5e-6 4.5e-6 4.5e-6 0 0 0 ref_p = 11 1 1 1 1 Is there anything wrong with my parameter? or should I use ref_p = 11 1 0 0 0 I saw someone use this ref_p before. tau_p and ref_p only take one parameter. The form for compressibility varies with pcoupletype. See manual section 7.3.14 Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
