[gmx-users] multi problem
Dear gmx users, I have problems in running a simulation on several nodes using the -multi option: I make the .tpr files for different temperatures (I want to use the REMD code) grompp -f param0.mdp -po param0.out.mdp -c conf.gro -p topol.top -o sim0.tpr grompp -f param1.mdp -po param1.out.mdp -c conf.gro -p topol.top -o sim1.tpr grompp -f param2.mdp -po param2.out.mdp -c conf.gro -p topol.top -o sim2.tpr . . . grompp -f paramN.mdp -po paramN.out.mdp -c conf.gro -p topol.top -o simN.tpr where N is the number of nodes in my cluster (P4 with gigabit ethernet) After the collection of input .tpr files are generated I start the simulations with: mpirun -np N mdrun_mpi -np N -multi -replex 2000 -s sim.tpr -o sim.trr ... but the program stops saying that it cannot find the sim1.tpr, sim2.tpr It do *FINDS* the sim0.tpr for the node where I start the simulation but for the rest of nodes it doesn't. I tried to put the simulation on a multi core machine (2 cores) and it works fine for N=2. But when I link 2 multicore machines the program stops with the same message except that the first .tpr file not found is the one corresponding to the second machine. I saw on the list that there were similar problems in the past but I didn't find any solution to them. I tried to soft link the mdrun_mpi executable in the working directory but the problem persists. Any help to solve this problem? Thanks a lot, Andrei ___ 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] multi problem
Andrei Neamtu wrote: Dear gmx users, I have problems in running a simulation on several nodes using the -multi option: I make the .tpr files for different temperatures (I want to use the REMD code) grompp -f param0.mdp -po param0.out.mdp -c conf.gro -p topol.top -o sim0.tpr grompp -f param1.mdp -po param1.out.mdp -c conf.gro -p topol.top -o sim1.tpr grompp -f param2.mdp -po param2.out.mdp -c conf.gro -p topol.top -o sim2.tpr . . . grompp -f paramN.mdp -po paramN.out.mdp -c conf.gro -p topol.top -o simN.tpr where N is the number of nodes in my cluster (P4 with gigabit ethernet) After the collection of input .tpr files are generated I start the simulations with: mpirun -np N mdrun_mpi -np N -multi -replex 2000 -s sim.tpr -o sim.trr ... but the program stops saying that it cannot find the sim1.tpr, sim2.tpr It do *FINDS* the sim0.tpr for the node where I start the simulation but for the rest of nodes it doesn't. Have you made sure the other nodes are using the same working directory and/or its contents are being propagated properly? Each MPI process tries to load a different .tpr and (at least) the correct one needs to be accessible from any given node. I tried to put the simulation on a multi core machine (2 cores) and it works fine for N=2. But when I link 2 multicore machines the program stops with the same message except that the first .tpr file not found is the one corresponding to the second machine. I saw on the list that there were similar problems in the past but I didn't find any solution to them. I tried to soft link the mdrun_mpi executable in the working directory but the problem persists. That isn't the problem - finding the .tpr is. 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] question about PBC and link cell based cutoff method
Dear GMX community! I have question about PBC and link cell based cutoff method. (1) for example one water molecule,if only H atom of one water molecule move out of box, however, O atom are still in the box. does this H atom will need to be image back to the box through PBC,or just ignore it until the mass center of one water move out of the box, then use PBC to image back to the box. how does the gromacs do! (2) I am confused about the link cell based cutoff method.i read some refs about this method,and it is very efficient.according to my understanding of precedure step1: divide the box into NxMxL cells. step2: put the all atoms into the cells step3: construct the neighboring cell index. If all the atoms do not move out of the whole box and do not apply PBC, i think this method is quite efficient. Actually, we should apply the PBC for every md step, does this mean that we should update step2 and step3 every md step. if the answer is yes, why the cell based cutoff method is more efficient relative to sphere based cutoff. how does the gromacs implement. Could anyone kindly help me to figure out these question. Thank you very much in advance! BEST REGARDS Fu 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
Re: [gmx-users] question about PBC and link cell based cutoff method
linfu wrote: > Dear GMX community! > > I have question about PBC and link cell based cutoff method. > > (1) > for example one water molecule,if only H atom of one water molecule > move out of box, however, O atom are still in the box. does this H atom > will need to be image back to the box through PBC,or just ignore it > until the mass center of one water move out of the box, then use PBC to > image back to the box. how does the gromacs do! > > (2) > I am confused about the link cell based cutoff method.i read some refs about > this method,and it is very efficient.according to my understanding of > precedure > step1: divide the box into NxMxL cells. > step2: put the all atoms into the cells > step3: construct the neighboring cell index. > If all the atoms do not move out of the whole box and do not apply PBC, i > think > this method is quite efficient. > Actually, we should apply the PBC for every md step, does this mean that we > should > update step2 and step3 every md step. if the answer is yes, why the cell > based cutoff > method is more efficient relative to sphere based cutoff. > how does the gromacs implement. > > Could anyone kindly help me to figure out these question. > Thank you very much in advance! It's hard to work out your problem, but it sounds like you haven't read manual section 3.2 yet. Please do so, and get back to us. 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] make-hole
Dear all I want to make hole in center of popc bilayer . how can i do it by make-hole program?(cx,cy=?) thanks 8:00? 8:25? 8:40? Find a flick in no time with the Yahoo! Search movie showtime shortcut. http://tools.search.yahoo.com/shortcuts/#news ___ 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:multi problem again
Dear Mark, Thank you for your reply! I thought that maybe the accessibility were the problem. I don't figure how to set the working directory of say node 1 to my current working directory on node 0. I setup node 1 to be able to access node 0 through ssh with no password but the problem remains. So .. I'm stuck here. Any idea where to start digging solving the most probable accessibility problem? In short there is how I made the GROMACS installation: 1. I installed GROMACS (serial and parallel version) on every node 2. I setup the node 0 to be able to access all other nodes through ssh without password 3. generated on node 0 the nodesfile file for lam booting I must say that parallel simulations run fine on the entire cluster (I mean a single system split on all nodes). The only problem appears when I try using -multi to simulate several copies of the system along the nodes. Do I have to use a file sharing system or something like this ...? It is the first time I try to use the -multi option. Thank you a lot, Andrei ___ 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] re:multi problem again
Andrei Neamtu wrote: Dear Mark, Thank you for your reply! I thought that maybe the accessibility were the problem. I don't figure how to set the working directory of say node 1 to my current working directory on node 0. I setup node 1 to be able to access node 0 through ssh with no password but the problem remains. So .. I'm stuck here. Any idea where to start digging solving the most probable accessibility problem? In short there is how I made the GROMACS installation: 1. I installed GROMACS (serial and parallel version) on every node 2. I setup the node 0 to be able to access all other nodes through ssh without password 3. generated on node 0 the nodesfile file for lam booting I must say that parallel simulations run fine on the entire cluster (I mean a single system split on all nodes). The only problem appears when I try using -multi to simulate several copies of the system along the nodes. Do I have to use a file sharing system or something like this ...? It is the first time I try to use the -multi option. Thank you a lot, Andrei you have to look into your queueing system. alternatively you can use the complete path e.g. /home/andrei/simulation/sim.tpr ___ 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 thewww 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
Re: [gmx-users] re:multi problem again
Setting up a NFS shall be handy. On 6/13/2007 5:13 PM, Andrei Neamtu wrote: Dear Mark, Thank you for your reply! I thought that maybe the accessibility were the problem. I don't figure how to set the working directory of say node 1 to my current working directory on node 0. I setup node 1 to be able to access node 0 through ssh with no password but the problem remains. So .. I'm stuck here. Any idea where to start digging solving the most probable accessibility problem? In short there is how I made the GROMACS installation: 1. I installed GROMACS (serial and parallel version) on every node 2. I setup the node 0 to be able to access all other nodes through ssh without password 3. generated on node 0 the nodesfile file for lam booting I must say that parallel simulations run fine on the entire cluster (I mean a single system split on all nodes). The only problem appears when I try using -multi to simulate several copies of the system along the nodes. Do I have to use a file sharing system or something like this ...? It is the first time I try to use the -multi option. Thank you a lot, Andrei ___ 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 thewww 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
Re: [gmx-users] Gromacs tools mistakenly change the name of atoms in coordinate files
Hi, I think that the terminal oxygen atoms should not be named OXT for the amber forcefields but rather OC1 and OC2. To check this look in the top folder at the ffamberXX.rtp file. Hope this helps Tom --On Tuesday, June 12, 2007 15:30 -0400 Robert Johnson <[EMAIL PROTECTED]> wrote: Hello everyone, I'm attempting to run a simulation of a protein that contains an atom named OXT (for the terminal oxygen atom). We are using the amber force field and have already successfully built a topology for the protein. However, when running Grompp we consistently receive the following error message: Warning: atom names in topology.top and coordinates.pdb don't match (OXT - O2) However, checking the actual files reveals that the atoms were initially named consistently. It seems that whenever we run various Gromacs programs (such as grompp or editconf), the OXT atom name is changed to O2. In other words, topology.top and coordinates.pdb both have the atom correctly named as OXT. It seems that Gromacs wants to substitute a "2" for the "XT". Does anyone know why Gromacs does this? Is this due to a bug in the code or is there some environment variable that defines XT=2? Thanks, Bob Johnson ___ 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 -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ 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:multi problem
Thanks a lot Mark and Ye, I will try both alternatives! Andrei ___ 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 38, Issue 29
>It's hard to work out your problem, but it sounds like you haven't read >manual section 3.2 yet. Please do so, and get back to us. > >Mark Thanks Mark! I will check manual. I am really sorry for bothering! 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
Re: [gmx-users] re:multi problem again
Andrei Neamtu wrote: Dear Mark, Thank you for your reply! I thought that maybe the accessibility were the problem. I don't figure how to set the working directory of say node 1 to my current working directory on node 0. I setup node 1 to be able to access node 0 through ssh with no password but the problem remains. So .. I'm stuck here. Any idea where to start digging solving the most probable accessibility problem? Like I said, you need to be able to see the run input file on a file system accessible to the other nodes. In short there is how I made the GROMACS installation: 1. I installed GROMACS (serial and parallel version) on every node 2. I setup the node 0 to be able to access all other nodes through ssh without password 3. generated on node 0 the nodesfile file for lam booting I must say that parallel simulations run fine on the entire cluster (I mean a single system split on all nodes). The only problem appears when I try using -multi to simulate several copies of the system along the nodes. This is consistent if in a non-multi parallel program, the file I/O is done only on the head node and the necessary information is propagated across MPI. I'm not sure if this is the case in GROMACS, however. 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
Re: [gmx-users] Gromacs tools mistakenly change the name of atoms in coordinate files
These are all fine points. However, the question I'm asking is why do Gromacs tools change atoms named OXT in PDB files to O2? Of course there are always workarounds i.e. just simply change the atom name in the coordinate file. However, I was wondering if anyone knew why this happened. I suppose I will submit a bugzilla. On 6/13/07, TJ Piggot <[EMAIL PROTECTED]> wrote: Hi, I think that the terminal oxygen atoms should not be named OXT for the amber forcefields but rather OC1 and OC2. To check this look in the top folder at the ffamberXX.rtp file. Hope this helps Tom --On Tuesday, June 12, 2007 15:30 -0400 Robert Johnson <[EMAIL PROTECTED]> wrote: > Hello everyone, > I'm attempting to run a simulation of a protein that contains an atom > named OXT (for the terminal oxygen atom). We are using the amber force > field and have already successfully built a topology for the protein. > However, when running Grompp we consistently receive the following > error message: > > Warning: atom names in topology.top and coordinates.pdb don't match (OXT > - O2) > > However, checking the actual files reveals that the atoms were > initially named consistently. It seems that whenever we run various > Gromacs programs (such as grompp or editconf), the OXT atom name is > changed to O2. In other words, topology.top and coordinates.pdb both > have the atom correctly named as OXT. It seems that Gromacs wants to > substitute a "2" for the "XT". > > Does anyone know why Gromacs does this? Is this due to a bug in the > code or is there some environment variable that defines XT=2? > > Thanks, > Bob Johnson > ___ > 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 -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ 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
Re: [gmx-users] Gromacs tools mistakenly change the name of atoms in coordinate files
Hi Robert, On Jun 13, 2007, at 6:48 PM, Robert Johnson wrote: These are all fine points. However, the question I'm asking is why do Gromacs tools change atoms named OXT in PDB files to O2? Of course there are always workarounds i.e. just simply change the atom name in the coordinate file. However, I was wondering if anyone knew why this happened. I suppose I will submit a bugzilla. Don't bother for now :-) This is because of a few old brain-dead choices in pdb2gmx, but we're working on replacing that completely, and then we'll be name-agnostic. The only thing I can say in our defense is that most other programs also push their own naming convention when generation hydrogens, etc. For instance, charmm will rename the resname of the first/last few atoms in each chain to NTER/CTER. 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
Re: [gmx-users] Gromacs tools mistakenly change the name of atoms in coordinate files
Robert Johnson wrote: These are all fine points. However, the question I'm asking is why do Gromacs tools change atoms named OXT in PDB files to O2? Of course there are always workarounds i.e. just simply change the atom name in the coordinate file. However, I was wondering if anyone knew why this happened. I suppose I will submit a bugzilla. you are welcome to submit a bugzilla, but for pdb2gmx this is the expected behavior. if you would like to change that you would have to edit database files. in principle naming should adhere to IUPAC/IUPAB standards (Biochemistry 9, 3471-3479 [1970]), but in practice there are at least four different naming schemes around only for hydrogens and other atoms (see http://www.bmrb.wisc.edu/ref_info/atom_nom.tbl). It seems that the GROMACS scheme (which is derived from GROMOS force field) is correct for the terminal oxygens. Almost all programs are wrong as regards hydrogen naming. -- 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] make-hole
I want to make hole in center of popc bilayer . how ?can i do it by make-hole program?(cx,cy=?) You can read the manual. Once you unpack the files you will have README.hole That file contains installation instructions (gromacs-3.1.4 only) and a link to usage instructions. ___ 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] Gromacs tools mistakenly change the name of atoms in coordinate files
On 6/14/2007 1:14 AM, Erik Lindahl wrote: Hi Robert, On Jun 13, 2007, at 6:48 PM, Robert Johnson wrote: These are all fine points. However, the question I'm asking is why do Gromacs tools change atoms named OXT in PDB files to O2? Of course there are always workarounds i.e. just simply change the atom name in the coordinate file. However, I was wondering if anyone knew why this happened. I suppose I will submit a bugzilla. Don't bother for now :-) This is because of a few old brain-dead choices in pdb2gmx, but we're working on replacing that completely, and then we'll be name-agnostic. The only thing I can say in our defense is that most other programs also push their own naming convention when generation hydrogens, etc. For instance, charmm will rename the resname of the first/last few atoms in each chain to NTER/CTER. Hi, Robert I am clueless why this topic has again made people upset about Gromacs. You may search for "David Mathog" in mailing list archive. e.g. http://www.gromacs.org/pipermail/gmx-users/2006-February/020087.html David, in the end, contributed some conversion script you might take a look. I admit that it is frustrated to add on more rules when I want to let pdb2gmx pass my PDB file. But when you are working with different force field, AMBER, CHARMM and OPLS-AA, like me, pdb2gmx will definitely have a dilemma to choose which atom instead of a fixed answer. Since, as you say, it is easy to change the atom name, why don't you do yourself? IMHO, it is rather to have a strict program which is faithful and rigid than to have an "smart" one which may induce errors. Of course, I believe Erik has a better idea to solve this problem. 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 thewww 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
Re: [gmx-users] Gromacs tools mistakenly change the name of atoms in coordinate files
I could understand if it was doing this within pdb2gmx or something that was constructing a topology file. I'm observing this behavior when using editconf to simply convert files to another format or apply box dimensions etc. Anyway, I submitted a bugzilla about it. This isn't such a big problem - make of it what you will. ;-) Bob On 6/13/07, Erik Lindahl <[EMAIL PROTECTED]> wrote: Hi Robert, On Jun 13, 2007, at 6:48 PM, Robert Johnson wrote: > These are all fine points. However, the question I'm asking is why do > Gromacs tools change atoms named OXT in PDB files to O2? Of course > there are always workarounds i.e. just simply change the atom name in > the coordinate file. However, I was wondering if anyone knew why this > happened. I suppose I will submit a bugzilla. Don't bother for now :-) This is because of a few old brain-dead choices in pdb2gmx, but we're working on replacing that completely, and then we'll be name-agnostic. The only thing I can say in our defense is that most other programs also push their own naming convention when generation hydrogens, etc. For instance, charmm will rename the resname of the first/last few atoms in each chain to NTER/CTER. 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 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] a question about output virial
Hello, From the mailinglist archive It is said the scalar virial from the g_energy vir=(1/3)*(vir(xx)+vir(yy)+vir(zz))=-0.5*sum(iinteractions are pairwised. I tried to verify this by using the relation PV=(2/3)*E(kin)+(1/3)*sum(iAll instantaneous virial, kinetic energy, pressure and volume can be obtained from g_energy. But I found the scalar virial I got using the first equation need to be multiplied by 3 to satisfy the second equation. That is to say, vir is actually -0.5*(1/3)*sum(ivir=(1/3)*(vir(xx)+vir(yy)+vir(zz)). Can anyone give any comments about this? Thanks! Lanyuan Lu _ 与联机的朋友进行交流，请使用 Live Messenger; http://get.live.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
[gmx-users] HB lifetime in g_hbond
Hi, I have a question regarding the calculation of hydrogen bond lifetimes in g_hbond: Line 1094 of gmx_hbond.c v 1.16.2.11 2006/04/02 (which is equivalent to line 1121 of gmx_hbond.c v 1.28 2006/08/30) reads: t = hb->time[i] - hb->time[0] - 0.5*dt; leading to the time series 1, 3, 5,.. that does not correspond to my sampling frequency of 2ps. This affects the calculation of x1 in the immediate next line. My question is: Why is t defined in this way? This question was posted in the past but did not find answer in the users list. Thanks! Patricia ___ 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] problem with the max number of atom in charge group
Hello everybody, I'm trying to use a DPPC bilayers with charges from the Jacob Sonne et al. study (Biophys J., 2007). The problem is that the authors have defined a single group for the whole DPPC molecule. This allow them to define new accurate charge for the head group atoms and the first atoms of the acyl chains. It is a problem with Gromacs which tolerate only 32 atoms per group (When I try to minimize my system, I've got the error : Max #atoms in a charge group...). In Gromacs, is it possible to defined groups with a net charge different form an integer, like 0.026042? Would it be a problem if I use PME? Note that the net charge of the molecule is still zero, of course. Thanks Nicolas -- [ Nicolas SAPAY, Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University drive NW, Calgary AB, T2N 1N4, Canada Tel: (403) 220-6869 Fax: (403) 289-9311 ___ 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] Warning when using both LJ and Buckingham non-bonded interaction
Hi, When I use both LJ and Buckingham non-bonded interaction in my topology file, specially like the following: [ nonbond_params ] ; ij func c6 c12 OW OW 1 ... ; ij func a bc6 CC2 ... When I run grompp using this topology file, I got such message: WARNING 2 [file "topol.top", line 26]: Trying to add BuckingHam while the default nonbond type is LJ (SR) Then is this topology OK? or I need other modifications? 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
Re: [gmx-users] problem with the max number of atom in charge group
Nicolas Sapay wrote: Hello everybody, I'm trying to use a DPPC bilayers with charges from the Jacob Sonne et al. study (Biophys J., 2007). The problem is that the authors have defined a single group for the whole DPPC molecule. This allow them to define new accurate charge for the head group atoms and the first atoms of the acyl chains. It is a problem with Gromacs which tolerate only 32 atoms per group (When I try to minimize my system, I've got the error : Max #atoms in a charge group...). In Gromacs, is it possible to defined groups with a net charge different form an integer, like 0.026042? Would it be a problem if I use PME? Note that the net charge of the molecule is still zero, of course. It would be possible, but as manual section 4.6.2 says, you now create net dipole moments in your system. I can't think of a reason it shouldn't be fairly easy to increase this maximum of 32. 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
Re: [gmx-users] Warning when using both LJ and Buckingham non-bonded interaction
WU Yanbin wrote: Hi, When I use both LJ and Buckingham non-bonded interaction in my topology file, specially like the following: [ nonbond_params ] ; ij func c6 c12 OW OW 1 ... ; ij func a bc6 CC2 ... When I run grompp using this topology file, I got such message: WARNING 2 [file "topol.top", line 26]: Trying to add BuckingHam while the default nonbond type is LJ (SR) Then is this topology OK? or I need other modifications? What single force field requires you to need to do this? There's no numerical problem, but the warning is there because you probably have an inappropriate model for your system. 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] Regarding scalling factor of cluster and installation in cluster
Dear gmx users, I have some problem regarding scalling factor of cluster. Here I have given cluster specifications, installation procedure, i request you go through query and suggest me. Here is the system specifications: Master node: Intel Pentium 4, 3.0 GHz with 64HT 800 MHz FSB/2 MB L2 Slave Nodes: Intel Xeon, 3.0 Ghz with HT 800 MHz FSB/2 MB L2 OS : Redhat Linux Enterprizes 4.0, 64 bit I downloaded fftw-3.0.1.tar.gz. and gromacs-3.3.1tar.gz from gromacs website. For parallel installation, I used the fallowing commands(in master node, in root), For fftw instalation.. ./configure --enable-float --enable-sse --enable-mpi make make install For gromacs installation.. ./configure --enable-mpi make make mdrun make install make install-mdrun make links It was installed in /opt/gromacs/ I didn't get any error messages To the gromacs in parallel, I have used the fallowing commands... grompp -f equilibrium.mdp -n index.ndx -p dopc.top -c dopc.pdb -np 5 -o dopc-eq.tpr mpirun -np 5 -machinefile gmxguest -nolocal /opt/gromacs/bin/mdrunmpi -s dopc-eq.tpr -c dopc-eq.pdb -o dopc-eq.trr (Note: gmxguest file contains five node names) I checked in 5 nodes, job is going in all nodes. The cluster took 22 hours to finish the job but same job with same time scale in with one Intel Pentium 4, 3.0 GHz , 64bit, rehat linux OS, it took 26 hours. My question is why it is happening, is there any problem in installing or gromacs not support this type of clusters. To improve scalling factor of cluster, what i have to do? Any suggestion is appreciated. Thank you in advance. with regards, Nagaraju Mulpuri. - Don't be flakey. Get Yahoo! Mail for Mobile and always stay connected to friends.___ 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: Warning when using both LJ and Buckingham non-bonded interaction
Hi, Everybody, And I found that if this simulation is on gromacs3.3, the warning becomes error. Yours Sincerely, WU Yanbin Message: 7 Date: Wed, 13 Jun 2007 21:35:42 -0500 From: "WU Yanbin" <[EMAIL PROTECTED]> Subject: [gmx-users] Warning when using both LJ and Buckingham non-bonded interaction To: gmx-users@gromacs.org Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Hi, When I use both LJ and Buckingham non-bonded interaction in my topology file, specially like the following: [ nonbond_params ] ; ij func c6 c12 OW OW 1 ... ; ij func a bc6 CC2 ... When I run grompp using this topology file, I got such message: WARNING 2 [file "topol.top", line 26]: Trying to add BuckingHam while the default nonbond type is LJ (SR) Then is this topology OK? or I need other modifications? 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
Re: [gmx-users] Regarding scalling factor of cluster and installation in cluster
naga raju wrote: Dear gmx users, I have some problem regarding scalling factor of cluster. Here I have given cluster specifications, installation procedure, i request you go through query and suggest me. Here is the system specifications: Master node: Intel Pentium 4, 3.0 GHz with 64HT 800 MHz FSB/2 MB L2 Slave Nodes: Intel Xeon, 3.0 Ghz with HT 800 MHz FSB/2 MB L2 OS : Redhat Linux Enterprizes 4.0, 64 bit I downloaded fftw-3.0.1.tar.gz. and gromacs-3.3.1tar.gz from gromacs website. For parallel installation, I used the fallowing commands(in master node, in root), For fftw instalation.. ./configure --enable-float --enable-sse --enable-mpi make make install For gromacs installation.. ./configure --enable-mpi make make mdrun make install make install-mdrun make links It was installed in /opt/gromacs/ I didn't get any error messages To the gromacs in parallel, I have used the fallowing commands... grompp -f equilibrium.mdp -n index.ndx -p dopc.top -c dopc.pdb -np 5 -o dopc-eq.tpr mpirun -np 5 -machinefile gmxguest -nolocal /opt/gromacs/bin/mdrunmpi -s dopc-eq.tpr -c dopc-eq.pdb -o dopc-eq.trr (Note: gmxguest file contains five node names) I checked in 5 nodes, job is going in all nodes. The cluster took 22 hours to finish the job but same job with same time scale in with one Intel Pentium 4, 3.0 GHz , 64bit, rehat linux OS, it took 26 hours. My question is why it is happening, is there any problem in installing or gromacs not support this type of clusters. To improve scalling factor of cluster, what i have to do? If you look at the bottom section of your log file, you'll see GROMACS report where it spent fractions of its time. It's also going to be less painful to test this stuff over two processors, rather than five, and over a short simulation, not a long one. IIRC "./configure --enable-mpi" won't install "/opt/gromacs/bin/mdrunmpi" either in that location or with that name so I suggest you look at config.log in the installation directory and report your actual configure line, not what you think you did :-) Otherwise, thanks for providing the details you did. You should test your cluster with some simple parallel code in which you can see the speedup, and report what hardware is doing your interconnects. 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
Re: [gmx-users] HB lifetime in g_hbond
Patricia Soto Becerra wrote: Hi, I have a question regarding the calculation of hydrogen bond lifetimes in g_hbond: Line 1094 of gmx_hbond.c v 1.16.2.11 2006/04/02 (which is equivalent to line 1121 of gmx_hbond.c v 1.28 2006/08/30) reads: t = hb->time[i] - hb->time[0] - 0.5*dt; leading to the time series 1, 3, 5,.. that does not correspond to my sampling frequency of 2ps. This affects the calculation of x1 in the immediate next line. My question is: Why is t defined in this way? The program computes an histogram and centers the points in between time points. Note that this flag gives you useless lifetimes, see J. Phys. Chem. B 110 pp. 4393-4398 (2006). You want to use the lifetime that comes from the -ac option (look at line with Forward) -- 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
Re: [gmx-users] Re: Warning when using both LJ and Buckingham non-bonded interaction
WU Yanbin wrote: Hi, Everybody, And I found that if this simulation is on gromacs3.3, the warning becomes error. Yours Sincerely, indeed, since this is not implemented. you canhowever use table potentials that differe between interaction pairs. -- 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
Re: [gmx-users] problem with the max number of atom in charge group
Nicolas Sapay wrote: Hello everybody, I'm trying to use a DPPC bilayers with charges from the Jacob Sonne et al. study (Biophys J., 2007). The problem is that the authors have defined a single group for the whole DPPC molecule. This allow them to define new accurate charge for the head group atoms and the first atoms of the acyl chains. It is a problem with Gromacs which tolerate only 32 atoms per group (When I try to minimize my system, I've got the error : Max #atoms in a charge group...). In Gromacs, is it possible to defined groups with a net charge different form an integer, like 0.026042? Would it be a problem if I use PME? Note that the net charge of the molecule is still zero, of course. Thanks Nicolas If you use PME than this is perfectly fine. You do not want charge groups larger than 3-4 atoms because the charge group is also used for neighborsearching, that means LJ interactions are between whole charge groups as well. -- 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
