[gmx-users] Re: gmx-users Digest, Vol 54, Issue 83
The easiest is to use antechamber to generate your topology and then use the amb2gmx.pl (http://www.alchemistry.org/wiki/index.php/Image:Amb2gmx.gz) To convert your amber topology to gromacs. sevaas Message: 2 > Date: Sat, 18 Oct 2008 00:23:07 -0200 > From: "Ragnarok sdf" <[EMAIL PROTECTED]> > Subject: [gmx-users] ffamber99 topologies for ligand > To: gmx-users@gromacs.org > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > How do I create topology files for a ligand when using ffamber99 in gromacs? > Thank you > Fabrcio Bracht > -- next part -- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20081018/597eb89b/attachment-0001.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
[gmx-users] RE: ligand parameterization for amber port in gmx
What do you mean by severe deformations? I would expect a lagere difference in conformation for pyrophosphate bound to mg and free pyrophosphate. You could do extra quantum calculations and compare them to your force field calculations to check the quality of your force field. If this is no good, you could consider using RESP charges. Did you compare your parameters do published pyrophosphate parameters e.g. http://www.pharmacy.manchester.ac.uk/bryce/amber hope this helps, servaas > Dear people, > > I have parameterized a ligand with one phosphate and one pyrophospate group > using antechamber with AM1-BCC charges and the GAFF forcefield. Amber files > were converted to gmx files (*.itp/*.top and *.gro) with the amb2gmx > conversion tool (http://www.alchemistry.org/wiki/index.php/Free_Energy_Tools) > and then used in gromacs for energy minimization. The geometry looks fine > after in vacuo EM and EM in water (ffamber tip3p model from amber ports) of > the ligand alone (not bound to protein!). Minimizing the ligand in its > binding mode as seen in the corresponding PDB (using the amber03 ff) also > works fine if magnesium ions are NOT included. Including magnesium ions > however leads to severe deformations of the phosphate and pyrophosphate > groups. I suspect it has something to do with not including the magnesium > ions in the parameterization. Can anybody please give me a hint on how to > solve this problem? > > Thanks a lot, > Merc ___ 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: gmx-users Digest, Vol 51, Issue 21
In the [ defaults ] section change the combination rule. servaas Hi, > > Is there a possibility when constructing the own .itp file to point > out Lennard-Jones (12, 6) parameters not in the form of C6 and C12 but > as sigma and epsilon. > > Is there any key to switch this option? > > Thanks. > > -- > Vitaly V. Chaban > School of Chemistry > National University of Kharkiv > Svoboda sq.,4, Kharkiv 61077, Ukraine > email: [EMAIL PROTECTED] > skype: vvchaban > > ___ 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: Dynamics : ONE dihedral angle time resolution
Or add option -all if you have several... servaas Message: 2 Date: Thu, 03 Jul 2008 10:36:56 +0200 From: "Xavier Periole" <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Dynamics : ONE dihedral angle time resolution To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain;charset=utf-8;format="flowed" On Thu, 3 Jul 2008 01:01:53 -0700 "Chih-Ying Lin" <[EMAIL PROTECTED]> wrote: Hi I want to get the dynamics of ONE dihedral angle time resolution. g_angle computes the angle distribution for a number of angles or dihedrals. With option -ov I can plot the average angle of a group of angles as a function of time. I don't want the average angle of a group of dihedral angle as a function of time. But, I need ONE dihedral angle as a function of time to know the dynamics of this dihedral angle. if you put only one angle in your index, then the average is the value of the angle in function of time. Thanks a lot Lin ___ 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 - XAvier Periole - PhD Molecular Dynamics Group / NMR and Computation University of Groningen The Netherlands - -- ___ 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: centering molecule in the water box
What box type are you using? Try adding following options -center -pbc mol -ur compact kind regards, servaas Hi all, During my MD the molecule experience a drift. Now I want to put the molecule at the center of the water box. I tried with trjconv using the -pbc mol and -center flag and using a reference frame where the molecule is at the center of the box. It seems that all the box (water+molecule) is translated, and so the position of the molecule relatively to the box is unchanged. I also checked the gmx-users list and I didn't get any useful suggestion. Fabio ___ 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] trjcat -demux
Dear gromacs users, I tried using trjcat like this: trjcat -f gromacs*.trr -demux replica_index.xvg (see below for replica_index.xvg and logfile) there are 20 trajectories containing each 2001 frames, with timestep of 0.5ps (I checked it with gmxcheck). The error: Reading frame 60 time1.500 Segmentation fault (frame doesn't fit with the time...) this is my replica_index.xvg file (it contains, 2001 lines with timestep of 0.5ps): 0 0123456789 10 11 12 13 14 15 16 17 18 19 0.5 013425679 108 11 12 13 14 16 15 17 19 18 . . . . 999.5 120614385 189 13 162 10 177 11 19 15 14 1000.0 120614385 189 13 162 10 177 11 19 15 14 This is the logfile: :-) trjcat (-: Option Filename Type Description -f gromacs20.trr Input, Mult. gromacs210.trr gromacs211.trr gromacs212.trr gromacs213.trr gromacs214.trr gromacs215.trr gromacs216.trr gromacs217.trr gromacs218.trr gromacs219.trr gromacs21.trr gromacs22.trr gromacs23.trr gromacs24.trr gromacs25.trr gromacs26.trr gromacs27.trr gromacs28.trr gromacs29.trr Generic trajectory: xtc trr trj gro g96 pdb -otrajout.xtc Output, Mult. Generic trajectory: xtc trr trj gro g96 pdb -n index.ndx Input, Opt. Index file -demux replica_index.xvg Input, Opt! xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -niceint19 Set the nicelevel -tu enum ps Time unit: ps, fs, ns, us, ms or s -[no]xvgrbool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -b time -1 First time to use (ps) -e time -1 Last time to use (ps) -dt time 0 Only write frame when t MOD dt = first time (ps) -precint3 Precision for .xtc and .gro writing in number of decimal places -[no]vel bool yes Read and write velocities if possible -[no]settime bool no Change starting time interactively -nrepl int1 Number of replicas assumed to be numbered consecutively. Only used with the -demux option -[no]sortbool yes Sort trajectory files (not frames) -[no]keeplast bool no keep overlapping frames at end of trajectory -[no]cat bool no do not discard double time frames Read 20 sets of 2000 points, dt = 0.5 trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 Reading frame 60 time1.500 Segmentation fault ___ 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] pbc-replica exchange-trjconv
For a given temperature, I will make them continues again then before analysis. Thanks for the help! kind regards, servaas Hoi Servaas, Was that the trajectory for a given temperature, or for a given system? It should be for the latter, as otherwise, there will be weird shifts introduced. A trajectory for a given system, over the different conditions should be (from the PBC point of view) continuous and it should be possible to perform PBC related operations. Hope it helps, Tsjerk ___ 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: pbc-replica exchange-trjconv
Tsjerk and Justin thanks for your suggestions. Justin, the combination you suggested did not work, I tried many things without succes here. I got the following error using whole and mol. (after doing nojump) There were 8 inconsistent shifts. Check your topology There were 8 inconsistent shifts. Check your topology Will stop reporting inconsistent shifts Tsjerk you are right I should explain the names: trjconv -f gromacs.trr -o cluster.trr -n lig_prot.ndx -pbc cluster -s top140.tpr gromacs.trr = trajectory generated by replica exchange cluster.trr = output name lig_prot.ndx=index file of with a group for ligand and protein top140.tpr=tpr file generated using the starting configuration of gromacs.trr You were right about the fit last time, but the error stays the same if I don't do the fit first... Could the it be the fact that it is a replica exchange simulation that causes the problem, this makes that there are jumps in the trajectory of course... kind regards, servaas servaas michielssens wrote: Dear gromacs users, I have a problem that is already discussed a lot on the mailing list, in a protein-ligand simulation the ligad jumps out of the box. The trajectory is generated by replica exchange simulation. So I used trjconv with the option cluster: trjconv -f fit.trr -o cluster.trr -n lig_prot.ndx -pbc cluster -s top140.tpr The program seems to get stuck at frame 208, repeating the following lines: COM:1.730 1.730 2.447 iter = 6214 Isq = 21.428 COM:0.000 0.000 0.000 iter = 6215 Isq = 54.757 COM:1.730 1.730 2.447 iter = 6208 Isq = 21.428 COM:0.000 0.000 0.000 iter = 6209 Isq = 54.757 COM:1.730 1.730 2.447 iter = 6210 Isq = 21.428 COM:0.000 0.000 0.000 iter = 6211 Isq = 54.757 COM:1.730 1.730 2.447 iter = 6212 Isq = 21.428 if I use this command: trjconv -f fit.trr -o cluster.trr -n lig_prot.ndx -pbc cluster The program runs but the ligands is still out of the box, the option -s seems to be necessary, but not working in my case. I also tried the -nojump option and after this the whole option but in visualistion (with VMD) I got strange bonds... I've found that sometimes several iterations of trjconv are necessary to get such things fixed up. Something like -pbc nojump, followed by 'whole,' and 'mol' or 'res' after that might do the trick. It's a bit of trial and error, and if anyone else out there has a better method, I'd love to hear it, too :-) -Justin An often reported problem was that the the structure in the tpr file is not close enough to the starting structure in the trajectory, I tried it by making a tpr file with a the strating structure of the trajectory (in this structure the ligand is in the active site if I look at the structure). But this did not help. What I am doing wrong here? thanks in advance for your help! kind regards, servaas ___ Hi Servaas, trjconv -f fit.trr -o cluster.trr -n lig_prot.ndx -pbc cluster -s top140.tpr I think there's quite a bit of reason to start calling you names here :) Assumedly, fit.trr means that it results from fitting the trajectory to a reference? So what does this do with your PBC? I also tried the -nojump option and after this the whole option but in visualistion (with VMD) I got strange bonds... Right, so strange bonds should be quite an indication that there's something weird with your shifts. An often reported problem was that the the structure in the tpr file is not close enough to the starting structure in the trajectory, I tried it by making a tpr file with a the strating structure of the trajectory (in this structure the ligand is in the active site if I look at the structure). But this did not help. Another often, or at least several times, mentioned problem relates to the fact that fitting a structure reorients the molecule, but leaves the PBC as it is, causing a mismatch between the system and the PBC. Therefore one can not execute any PBC related operations (nojump, cluster, whole), after the trajectory has been fitted. No hard feelings ;) Cheers, Tsjerk ___ 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] pbc-replica exchange-trjconv
Dear gromacs users, I have a problem that is already discussed a lot on the mailing list, in a protein-ligand simulation the ligad jumps out of the box. The trajectory is generated by replica exchange simulation. So I used trjconv with the option cluster: trjconv -f fit.trr -o cluster.trr -n lig_prot.ndx -pbc cluster -s top140.tpr The program seems to get stuck at frame 208, repeating the following lines: COM:1.730 1.730 2.447 iter = 6214 Isq = 21.428 COM:0.000 0.000 0.000 iter = 6215 Isq = 54.757 COM:1.730 1.730 2.447 iter = 6208 Isq = 21.428 COM:0.000 0.000 0.000 iter = 6209 Isq = 54.757 COM:1.730 1.730 2.447 iter = 6210 Isq = 21.428 COM:0.000 0.000 0.000 iter = 6211 Isq = 54.757 COM:1.730 1.730 2.447 iter = 6212 Isq = 21.428 if I use this command: trjconv -f fit.trr -o cluster.trr -n lig_prot.ndx -pbc cluster The program runs but the ligands is still out of the box, the option -s seems to be necessary, but not working in my case. I also tried the -nojump option and after this the whole option but in visualistion (with VMD) I got strange bonds... An often reported problem was that the the structure in the tpr file is not close enough to the starting structure in the trajectory, I tried it by making a tpr file with a the strating structure of the trajectory (in this structure the ligand is in the active site if I look at the structure). But this did not help. What I am doing wrong here? thanks in advance for your help! kind regards, servaas ___ 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] system contains proteins and DNAs with ffamber99
If you have amber, you can make your topology in amber and convert them to gromacs with the script on this website: http://chemistry.csulb.edu/ffamber/tools.html kind regards, servaas Dear all, Sometimes,the PDB file contains water molecules which only have the oxygen atom. Can Gromacs add the hydrogen atoms of the water molecules? Additionly, when use Gromacs with the force field ffamber99, Can it add the hydrogen atoms of the DNA? Can I use the force field ffamber99 to simulate the system which contains proteins and DNAs? Best regards, ___ 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: Help needed on using general amber force field (GAFF)
There is not really a difference between proper and improper dihedrals in amber the amberFF, the only difference is that improper dihedrals are not serially linked (amber 8 manual page 261). I do not really understand your problem. Are you writing a new topology for a small molecule in the amberFF? You can best use the amber tools in this case and then convert it to gromacs with the script on the website I mentioned below. If you rename your atoms in the amber conventions you can use parmchk to check if parameters are present in de gaff. If not you can calculate them by quantum chemical chemical calculation or use equivalent parameters. (but this is more a topic for the amber mailing list...) kind regards, servaas Message: 6 Date: Mon, 31 Mar 2008 10:25:17 -0400 From: "Xiangyu Fan" <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Re: Help needed on using general amber force field (GAFF) in Gromacs To: "Discussion list for GROMACS users" Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Hi Servaas, Thanks for your reply. Your inforamtion is very helpful. Now I am trying to write the topology file by myself when dealing with a small molecule. I have know their conversion relationship, but in my case, I want to fix a few atoms in a plane. From the gaff.dat file , I can see the parameters on proper dihedral but not improper dihedral. I am just wondering how to retrival info. on improper dihedral from gaff.dat file. If you have such experience, please let me know. I do appreciate your kind help. best regards, Xiangyu On 3/14/08, servaas michielssens <[EMAIL PROTECTED]> wrote: I don't think you can generate your topology from the pdb file with gromacs in this case (with gaff). You can first make it in amber and than convert it to gromacs. On this website is the info you need, in the FAQs there is a link to dowload the script to do the job. http://chemistry.csulb.edu/ffamber/ kind regards, servaas ___ 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: Help needed on using general amber force field (GAFF) in Gromacs
I don't think you can generate your topology from the pdb file with gromacs in this case (with gaff). You can first make it in amber and than convert it to gromacs. On this website is the info you need, in the FAQs there is a link to dowload the script to do the job. http://chemistry.csulb.edu/ffamber/ kind regards, servaas Date: Thu, 13 Mar 2008 22:57:29 -0400 From: "Xiangyu Fan" <[EMAIL PROTECTED]> Subject: [gmx-users] Help needed on using general amber force field (GAFF) in Gromacs To: gmx-users@gromacs.org Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Hi all, I am using GAFF force field for Gromacs package to simulate MD of surfactant molecule. I know we can generate .top file using some simple command like pdb2gmx if we use gromos force field. I am just wondering whether I can do the similar thing when using GAFF force field. If you have any experience in GAFF+Gromacs, please give me some advice. thanks Xiangyu Fan UNC-Chapel Hill -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20080313/1cd1d95e/attachment-0001.html -- Message: 6 Date: Fri, 14 Mar 2008 12:30:27 +0800 From: Yang Ye <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Help needed on using general amber force field (GAFF)in Gromacs To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed You might not use pdb2gmx for such task. Once you have generated topology in AMBER format with Antechamber in GAFF, you will need to use some tools like ambconv.pl or ambconv (one is Perl script and one is a C++ programme, check GROMACS' website) to convert those files into GROMACS format. There is ffamber, a port for AMBER force field to GROMACS, which largely similar to what ambconv.pl or ambconv produces. They will provide force field for protein and nuclei acids through pdb2gmx. With some hand-modifications to the files, you can combine ambconv and ffamber, so you have a solution for almost all molecules. Regards, Yang Ye Xiangyu Fan wrote: > Hi all, > > I am using GAFF force field for Gromacs package to simulate MD of > surfactant molecule. I know we can generate .top file using some > simple command like pdb2gmx if we use gromos force field. I am just > wondering whether I can do the similar thing when using GAFF force > field. If you have any experience in GAFF+Gromacs, please give me some > advice. thanks > > Xiangyu Fan > > UNC-Chapel Hill > > > > > ___ > 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] gromacs versus amber boxsize
I ran the following command in gromacs: editconf -bt dodecahedron -f p61_vac_gro.gro -o p61_vac_dod.gro -d 0.8 The equivalent command in amber: solvateoct p61_vac.pdb TIP3PBOX 8.0 As far as I understand this, both command created a box were the edges are 0.8 nm away from the solute. But the resulting image distance (d in the manual) in gromacs is: 121.3092 and in amber: 85.9385483 This is makes a hugde difference in the number of water atoms to add. Does anyone has an explanation for this paradox? kind regards, servaas___ 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] gromacs versus amber boxsize -correction-
I made a mistake in the numbers, but the question remains: I ran the following command in gromacs: editconf -bt dodecahedron -f p61_vac_gro.gro -o p61_vac_dod.gro -d 0.8 The equivalent command in amber: solvateoct p61_vac.pdb TIP3PBOX 8.0 As far as I understand this, both command created a box were the edges are 0.8 nm away from the solute. But the resulting image distance (d in the manual) in gromacs is: 121.3092 and in amber: 110.5103716 This is makes a hugde difference in the number of water atoms to add. Does anyone has an explanation for this paradox? kind regards, servaas___ 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: parallel simulation crash on 6 processors
> -- next part -- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20071128/e80a1638/attachment-0001.html > > -- > > Message: 5 > Date: Wed, 28 Nov 2007 14:39:29 +0100 > From: David van der Spoel <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] parallel simulation crash on 6 processors > To: Discussion list for GROMACS users > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > servaas michielssens wrote: > > I tried to run a gromacs simulation (gromacs 3.3.1, MD, 18000 atoms) on > > 2 systems: > > > > Intel(R) Pentium(R) CPU 2.40GHz with 100Mbit network > > and > > AMD Opteron(tm) Processor 250 with 1Gbit network > > On both systems I had a crash when I tried to run with more then 5 > > processors. From 1-5 there was no problem. > > > more details please. > > I ran same the simulation on 1,2,3,4 and 5 processors without any problem, so I there is no problem with the system that I'm using. But from to moment I tried to use 6 processors of the same cluster the simulation crashes, this is the error: Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 6 On AMD: [0] MPI Abort by user Aborting program ! [0] Aborting program! p4_error: latest msg from perror: No such file or directory p0_3303: p4_error: : -1 Killed by signal 2.^M Killed by signal 2.^M Killed by signal 2.^M Killed by signal 2.^M Killed by signal 2.^M p0_3303: (1.088153) net_send: could not write to fd=4, errno = 32 error while executing run nb 1 On intel: p4_1781: p4_error: Timeout in establishing connection to remote process: 0 rm_l_4_1786: (318.577125) net_send: could not write to fd=5, errno = 32 p4_1781: (318.580132) net_send: could not write to fd=5, errno = 32 p0_26458: (319.239545) net_recv failed for fd = 8 p0_26458: p4_error: net_recv read, errno = : 104 Killed by signal 2.^M Killed by signal 2.^M Killed by signal 2.^M Killed by signal 2.^M Killed by signal 2.^M p0_26458: (325.249810) net_send: could not write to fd=4, errno = 32 error while executing run nb 1 hope this is the information you need, greets, servaas > > kind regards, > > > > servaas michielssens > > > > > > > > > > ___ > > 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 > > > -- > David. > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596,75124 Uppsala, Sweden > phone:46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > > ___ 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] parallel simulation crash on 6 processors
I tried to run a gromacs simulation (gromacs 3.3.1, MD, 18000 atoms) on 2 systems: Intel(R) Pentium(R) CPU 2.40GHz with 100Mbit network and AMD Opteron(tm) Processor 250 with 1Gbit network On both systems I had a crash when I tried to run with more then 5 processors. From 1-5 there was no problem. kind regards, servaas michielssens___ 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: gmx-users Digest, Vol 43, Issue 81
Date: Wed, 21 Nov 2007 14:03:53 -0800 From: "David Mobley" <[EMAIL PROTECTED]> Subject: Re: [gmx-users] restart an amber run in gromacs To: "Discussion list for GROMACS users" Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1 Hi, servaas michielssens wrote: > I used amb2gmx.pl (from http://chemistry.csulb.edu/ffamber/) to convert > an amber topology and restart file to a gromacs topology and structure > file and tried to continue the simulation in gromacs. I got the > following error message: > > Constraint error in algorithm Lincs at step 0 > > t = 0.000 ps: Water molecule starting at atom 4642 can not be settled. > Check for bad contacts and/or reduce the time-step. Wrote pdb files > with > previous and current coordinates > > It seems strange to me that this error occurs as there was no problem > with this simulation in amber. (it ran a few ns in amber). > I tried to run it after minimalization and this worked fine. So there > seems to be a problem while converting the files, I am new to gromacs > and I don't really have a clue how to find the cause of this problem, > perhaps some of you also tried to continue a amber run in gromacs? The script is not intended for continuing AMBER runs in GROMACS. As far as I know no one has ever tested it on this. There are a number of reasons why this would not be a good idea, not the least of which is that you are changing simulation parameters/algorithms when you do so, as Mark notes in the following paragraph. Judging by my interpretation of your last email, you probably did a more radical change of ensemble than you think you did. Both AMBER and GROMACS are approximating some true ensemble, and there's no reason to assume that a configuration from one will be equilibrated in the other. Also, I personally have never used the script to convert an entire system including solvent from AMBER to GROMACS -- just proteins and ligands, for example, One might worry that the simulation box will not be converted correct, which could certainly lead to the problems you're seeing. Short answer: Even if you think the script is working perfectly, converting the box properly, etc., then you should at the very least minimize and equilibrate your amber end state before doing production in gromacs. David Mark Thanks for your help, I checked the perl script (amb2gmx.pl) it should work for a solvated protein. The solvend and box are converted to gromacs but the box information is not converted as it should, amber only defines d and 3 angels (+information in the topology that it deals with a truncated octahedron), while gromacs needs 3 vectors to defines a truncated octahedron and this information is only in the .gro file not in the topology. The amb2gmx.pl script only copies tree values to the .gro file for an truncated octahedron so gromacs thinks it is a cubic box. Normally the ensembles are both NTP, I can hardly believe that differnces in algoritm would cause a "Constraint error in algorithm Lincs at step 0" and make the simulation crash. But I agree that this procedure is not the way to go for a good simulation, the only intention of this was doing a speed comparision. kind regards, servaas ___ 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:Re: gromacs preformance versus amber (David van der Spoel)
Message: 1 Date: Wed, 21 Nov 2007 21:54:57 +0100 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] gromacs preformance versus amber To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed servaas michielssens wrote: I am considering to use gromacs for MD-simulation for speed reasons, so I tried to compare a amber simulation to a gromacs simulation. I ran a 20ps simulation with amber. I converted my topology and coordinate file from amber to gromacs using and tried the same run in gromacs. amb2gmx.pl(http://chemistry.csulb.edu/ffamber/). This is my amber input: &cntrl imin=0,nstlim=1,nmropt=0 irest=1,ntx=5, iwrap=1, nscm=1000, dt=0.002, ntb=2,ntp=1, ntt=1,tautp=1.0,temp0=300.0, ntc=2,ntf=2, cut=8.0, ntwx=250,ntpr=250, / This is my gromacs input: title = FWS cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 1 ; total 20 ps. nstcomm = 1000 nstxout = 250 ; collect data every 1 ps nstlog = 0 nstenergy = 250 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cutoff rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on Tcoupl = berendsen tau_t = 1.0 1.0 tcgrps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = parrinellorahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = no gen_temp= 300.0 gen_seed= 937475 I ran it on 4 AMD Opteron(tm) Processor 250. It turned out that amber could simulate 1.5ns/day and gromacs only 1ns/day. This was a surprise to me, I expected that gromacs would be faster. Could it be that using gromacs with the amberFF is not faster than just using amber? I am new to gromacs and perhaps I didn't compare them correct. Did you run gromacs in parallel at all? Did you get four md.log files, one for each processor? Thanks for you answer, Yes this worked fine, I have a log file for every processor, their must be some other problem. I also tried to run it on 8 or 16 processors, here the run failed. Amber runs worked fine, so I don't think their are problems with the processors kind regards, servaas michielssens. ___ 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] restart an amber run in gromacs
I used amb2gmx.pl (from http://chemistry.csulb.edu/ffamber/) to convert an amber topology and restart file to a gromacs topology and structure file and tried to continue the simulation in gromacs. I got the following error message: Constraint error in algorithm Lincs at step 0 t = 0.000 ps: Water molecule starting at atom 4642 can not be settled. Check for bad contacts and/or reduce the time-step. Wrote pdb files with previous and current coordinates It seems strange to me that this error occurs as there was no problem with this simulation in amber. (it ran a few ns in amber). I tried to run it after minimalization and this worked fine. So there seems to be a problem while converting the files, I am new to gromacs and I don't really have a clue how to find the cause of this problem, perhaps some of you also tried to continue a amber run in gromacs? kind regards, servaas michielssens ___ 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] restart amber run in gromacs
I used amb2gmx.pl (from http://chemistry.csulb.edu/ffamber/) to convert an amber topology and restart file to a gromacs topology and structure file and tried to continue the simulation in gromacs. I got the following error message: Constraint error in algorithm Lincs at step 0 t = 0.000 ps: Water molecule starting at atom 4642 can not be settled. Check for bad contacts and/or reduce the time-step. Wrote pdb files with previous and current coordinates It seems strange to me that this error occurs as there was no problem with this simulation in amber. (it ran a few ns in amber). I tried to run it after minimalization and this worked fine. So there seems to be a problem while converting the files, I am new to gromacs and I don't really have a clue how to find the cause of this problem, perhaps some of you also tried to continue a amber run in gromacs? kind regards, servaas michielssens ___ 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] gromacs preformance versus amber
I am considering to use gromacs for MD-simulation for speed reasons, so I tried to compare a amber simulation to a gromacs simulation. I ran a 20ps simulation with amber. I converted my topology and coordinate file from amber to gromacs using and tried the same run in gromacs. amb2gmx.pl(http://chemistry.csulb.edu/ffamber/). This is my amber input: &cntrl imin=0,nstlim=1,nmropt=0 irest=1,ntx=5, iwrap=1, nscm=1000, dt=0.002, ntb=2,ntp=1, ntt=1,tautp=1.0,temp0=300.0, ntc=2,ntf=2, cut=8.0, ntwx=250,ntpr=250, / This is my gromacs input: title = FWS cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 1 ; total 20 ps. nstcomm = 1000 nstxout = 250 ; collect data every 1 ps nstlog = 0 nstenergy = 250 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cutoff rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on Tcoupl = berendsen tau_t = 1.0 1.0 tcgrps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = parrinellorahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = no gen_temp= 300.0 gen_seed= 937475 I ran it on 4 AMD Opteron(tm) Processor 250. It turned out that amber could simulate 1.5ns/day and gromacs only 1ns/day. This was a surprise to me, I expected that gromacs would be faster. Could it be that using gromacs with the amberFF is not faster than just using amber? I am new to gromacs and perhaps I didn't compare them correct. kind regards, servaas michielssens ___ 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
