[gmx-users] pair forces
Hi everyone! I'm trying to get the value for the force (sum of all forces) between two specific atoms (which I have defined in two index, energy and charge groups). I've tried using g_energy (also with the -pairs option which I think may be irrelevant here). Does anyone have an idea how to get the information I want? Thanks, -- Inon Sharony ינון שרוני +972(3)6407634 atto.TAU.ac.IL/~inonshar Please consider your environmental responsibility before printing this e-mail. ___ 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] seek for forcefield parameters
hi,gmx-users, I would like to study hydrogen bond in acetaldehyde system with Opls-AA force-field. But I found that the charge of hydrogen connecting to carbonyl group in acetaldehyde is 0 in the Opls-AA force-field.So it is not fit for me. It will be appreciated if anybody can supply forcefield parameters of the acetaldehyde or some suggestion for me. Jinyao Wang [EMAIL PROTECTED] 2008-11-02 ___ 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 g_dist (probably solved)
Hi all, i had problems with g_dist. My system consists of 15 molecules urea with a short alkane linker. With constraints and restraintss (distance, angles and dihedrals) made it that the molecules are in one line (the last methyl-group of the alkan linker). Here a little picture: ... | | |... XX X ... | is the alkan linker; X is the urea-group and _ is the line which conacts the methyl-groups. The distance between each molecule is 2nm, so (with 15 molecules) the distance between the first and the last molecule should be 28nm. The size of the simulation box was 40 10 10 (all nm), with no pbc (periodic boundary conditions) (the 'line' was along the x-axis). When i determined the distance between the first and the last molecule with g_dist, the program gave some errors: There were 1 inconsistent shifts. Check your topology , but the program ended normally. The calculeted distance was around 12nm (versus the 28nm which is the correct value; i calculated it from the .gro file). So my idea was the g_dist uses pbc to calculate the distance (even if the simulation had no pbc). The distance between the first and the last methyl-group (in the two nearest boxes) should be around 40nm (box size) -28nm (distance in one box) = 12 nm (distaance over two boxes). Is this idea right?!? In another simulation i increased the box size to 60 60 60 (nm). Here g_dist had no troubles. I get no error messages (There were 1 inconsistent shifts. Check your topology) and the distance is right. The other question is: What does the error message mean? Thanks for your help. Thomas ___ 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 g_dist (probably solved)
Hi Thomas, To have PBC or not in a run has nothing to do with analysis. Analysis tools don't have a clue of what you put into the .mdp files. Any of tha analysis tools will assume that the box specified in the file involves PBC. Don't know from the top of my head, but I think where possibly necessary, tools offer an option -nopbc. If g_dist doesn't have that, it probably should :) (and in that case you might want to submit it to bugzilla). Cheers, Tsjerk On Sun, Nov 2, 2008 at 3:14 PM, Thomas Schlesier [EMAIL PROTECTED] wrote: Hi all, i had problems with g_dist. My system consists of 15 molecules urea with a short alkane linker. With constraints and restraintss (distance, angles and dihedrals) made it that the molecules are in one line (the last methyl-group of the alkan linker). Here a little picture: ... | | |... XX X ... | is the alkan linker; X is the urea-group and _ is the line which conacts the methyl-groups. The distance between each molecule is 2nm, so (with 15 molecules) the distance between the first and the last molecule should be 28nm. The size of the simulation box was 40 10 10 (all nm), with no pbc (periodic boundary conditions) (the 'line' was along the x-axis). When i determined the distance between the first and the last molecule with g_dist, the program gave some errors: There were 1 inconsistent shifts. Check your topology , but the program ended normally. The calculeted distance was around 12nm (versus the 28nm which is the correct value; i calculated it from the .gro file). So my idea was the g_dist uses pbc to calculate the distance (even if the simulation had no pbc). The distance between the first and the last methyl-group (in the two nearest boxes) should be around 40nm (box size) -28nm (distance in one box) = 12 nm (distaance over two boxes). Is this idea right?!? In another simulation i increased the box size to 60 60 60 (nm). Here g_dist had no troubles. I get no error messages (There were 1 inconsistent shifts. Check your topology) and the distance is right. The other question is: What does the error message mean? Thanks for your help. Thomas ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] pair forces
Inon Sharony wrote: Hi everyone! I'm trying to get the value for the force (sum of all forces) between two specific atoms (which I have defined in two index, energy and charge groups). I've tried using g_energy (also with the -pairs option which I think may be irrelevant here). Does anyone have an idea how to get the information I want? GROMACS does calculate pairwise forces and interaction energies by looping over groups, storing subtotals for energygrps, but it only calculates grand totals for forces. You could use the mdrun -rerun facility to get this. Run the normal simulation, and then another one after zeroing out the charge, vdW for all atoms other than the pair of interest, and all the bonded parameters. The only things left are the forces of that interacting pair, which you write to a trajectory file with nstfout. Caveat: no force fields were parameterized to model pairwise forces. They may do an OK job, because there were parameterized to reproduce quantities that are mostly likely to be accurate if the pairwise forces are also reasonable, but cancellation of compensating errors in individual pairwise forces could easily be occurring. 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] pdb file
He, Yang wrote: Hi all users, I just encountered a problem about the DNA model when I set the coordinate in the pdb file . It always shows very strange figure about the DNA model. My pdb file is like this: ATOM 1 Ab1 DNA 1 0.0510.575 0.516 1.0 0.0 ATOM 2 Tb1 DNA 1 0.1910.159 2.344 1.0 0.0 ATOM 3 S1 DNA 1 1.2802.365 6.568 1.0 0.0 ATOM 4 S2 DNA 1 1.280 -2.365-6.568 1.0 0.0 ATOM 5 P1 DNA 1 2.186 -0.628 8.896 1.0 0.0 ATOM 6 P2 DNA 1 2.186 -0.628-8.896 1.0 0.0 ATOM 7 S3 DNA 1 4.660 -1.947 6.704 1.0 0.0 ATOM 8 S4 DNA 1 4.6601.947-6.704 1.0 0.0 ATOM 9 Cb1 DNA 1 3.4310.162 0.756 1.0 0.0 ATOM 10 Gb1 DNA 1 3.571 -1.249 1.989 1.0 0.0 ATOM 11 P3 DNA 1 5.556 -5.737 6.828 1.0 0.0 ATOM 12 P4 DNA 1 5.5565.737-6.828 1.0 0.0 ATOM 13 S5 DNA 1 8.040 -5.516 4.279 1.0 0.0 ATOM 14 S6 DNA 1 8.0405.516-4.279 1.0 0.0 ATOM 15 Gb2 DNA 1 6.811 -1.814 1.407 1.0 0.0 ATOM 16 Cb2 DNA 1 6.951 -0.319 0.764 1.0 0.0 ATOM 17 P5 DNA 1 8.936 -8.655 2.152 1.0 0.0 ATOM 18 P6 DNA 1 8.9368.655-2.152 1.0 0.0 ATOM 19 S7 DNA 1 11.426.978 0.220 1.0 0.0 ATOM 20 S8 DNA 1 11.42 -6.978-0.220 1.0 0.0 ATOM 21 Tb2 DNA 1 10.191 -0.707 0.430 1.0 0.0 ATOM 22 Ab2 DNA 1 10.331 -2.237-0.518 1.0 0.0 CONECT 1 3 CONECT 2 4 CONECT 3 1 5 CONECT 4 2 6 CONECT 5 3 7 CONECT 6 4 8 CONECT 7 5 9 11 CONECT 8 6 10 12 CONECT 9 7 CONECT 10 8 CONECT 11 7 13 CONECT 12 8 14 CONECT 13 11 15 17 CONECT 14 12 16 18 CONECT 15 13 CONECT 16 14 CONECT 17 13 19 CONECT 18 14 20 CONECT 19 17 21 CONECT 20 18 22 CONECT 21 19 CONECT 22 20 MASTER00000000 22022 0 END Can anyone of you tell me whether there is something wrong with my pdb file? Your atom names look more like you have a bizarre cluster of sulfur and heavy atoms, not DNA. Also possible is that you have a united-atom model with about one site per nucleic acid residue. I've no idea whether any united-atom models of DNA exist. 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 4 for SunOS
DimitryASuplatov wrote: Hello, I am trying to compile mdrun from gromacs 4 package under Solaris 8. I compile fftw, then enter /gromacs and run ./compile --enable-mpi and make mdrun. Then I get the following error (see below). Googling did not help. http://www.google.com.au/search?q=GROMACS+XDR_INT_SIZE 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] Re: Persistent crashes due to unsettled waters
Thanks for the tip about the blowing-up page on the wiki--I already checked there and found little help because my crashes are coming so long into the runs (sometimes as late as 1 million steps in). This is also why I can't debug with nstxout = 1: the output files would get too big. I'm also reluctant to lower the time-step from 2 fs to say 1 fs, because I'm already resource-limited in these simulations, and slowing them down would halve the amount of sampling I could do. Any other thoughts on this? The mdp file for these crashing runs is shown below: integrator = md nsteps = 200 dt = 0.002 nstlist = 10 nstcomm = 1 rlist = 1.0 coulombtype = pme rcoulomb= 1.0 vdw-type= cut-off rvdw= 1.0 tcoupl = Nose-Hoover tc-grps = protein non-protein tau-t = 0.5 0.5 ref-t = 298 298 nstxout = 1000 nstxtcout = 100 nstenergy = 100 Message: 7 Date: Fri, 31 Oct 2008 20:43:22 -0400 From: Justin A. Lemkul [EMAIL PROTECTED] Subject: Re: [gmx-users] Persistent crashes due to unsettled waters To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Aaron Fafarman wrote: Dear GMX-community, I'm running four related, equilibrium-dynamics simulations of a small protein in explicit water, each with a different non-natural amino-acid in the sequence. One of the four non-natural amino-acid containing proteins can be simulated for long times, up to 4 ns without incident, but the other three invariably crash. On repeated reinitialization (changing the box size, changing the duration of position restrained refinement) they still keep crashing at any time between 100's of picoseconds and 2 ns. Usually an error such as 3009.270 ps: Water molecule starting at atom 26883 can not be settled. is printed to the log file and the pdb of the step after the crash has nonsense numbers for the coordinates of the offending water molecule. It's always a different water molecule, always a high-numbered atom (2). The crashes happen on both a self-compiled linux build and on a self-compiled Mac OS 10.4 build, both GMX 3.3.1. A simulation of just the parameterized amino acids in a box of water never crashes over the course of a 4 ns simulation so I don't suspect my amino-acid parameters. As a general reference, check out the following: http://wiki.gromacs.org/index.php/blowing_up For debugging purposes, I have found that if I set nstxout = 1 in the .mdp file, I can usually capture the initial events leading to the explosion. Unfortunately, the water molecule that cannot be settled is usually an unfortunate victim of another molecule that has gone flying off across your system. It might also be useful to post your .mdp file here if you are still unable to find the problem. -Justin ___ 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: Persistent crashes due to unsettled waters
Aaron Fafarman wrote: Thanks for the tip about the blowing-up page on the wiki--I already checked there and found little help because my crashes are coming so long into the runs (sometimes as late as 1 million steps in). This is also why I can't debug with nstxout = 1: the output files would get too big. I'm also reluctant to lower the time-step from 2 fs to say 1 fs, because I'm already resource-limited in these simulations, and slowing them down would halve the amount of sampling I could do. If you structure your calculation in batches of a few hundred picoseconds or so, then when something goes wrong, you've got a restart close beforehand. You can tweak that to get your debugging info for the part that failed. GROMACS 4.0's checkpointing facility might let you avoid doing lots of work here, but I haven't played with it yet. Coupled with the above, nstxtcout = 1 with xtcgroups on the whole system would be less resource-demanding. You could decide to throw away your debugging xtc after each successful batch, possibly after a trjconv to extract the bits of information you normally wanted to keep in your xtc files. Any other thoughts on this? The mdp file for these crashing runs is shown below: integrator = md nsteps = 200 dt = 0.002 nstlist = 10 nstcomm = 1 rlist = 1.0 coulombtype = pme rcoulomb= 1.0 vdw-type= cut-off rvdw= 1.0 tcoupl = Nose-Hoover tc-grps = protein non-protein tau-t = 0.5 0.5 ref-t = 298 298 nstxout = 1000 nstxtcout = 100 nstenergy = 100 Seems fine. Message: 7 Date: Fri, 31 Oct 2008 20:43:22 -0400 From: Justin A. Lemkul [EMAIL PROTECTED] Subject: Re: [gmx-users] Persistent crashes due to unsettled waters To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Aaron Fafarman wrote: Dear GMX-community, I'm running four related, equilibrium-dynamics simulations of a small protein in explicit water, each with a different non-natural amino-acid in the sequence. One of the four non-natural amino-acid containing proteins can be simulated for long times, up to 4 ns without incident, but the other three invariably crash. On repeated reinitialization (changing the box size, changing the duration of position restrained refinement) they still keep crashing at any time between 100's of picoseconds and 2 ns. Usually an error such as 3009.270 ps: Water molecule starting at atom 26883 can not be settled. is printed to the log file and the pdb of the step after the crash has nonsense numbers for the coordinates of the offending water molecule. It's always a different water molecule, always a high-numbered atom (2). The crashes happen on both a self-compiled linux build and on a self-compiled Mac OS 10.4 build, both GMX 3.3.1. A simulation of just the parameterized amino acids in a box of water never crashes over the course of a 4 ns simulation so I don't suspect my amino-acid parameters. One consistent hypothesis that isn't tested above is that you've got some kind of erroneous long-range interaction that might only be manifest when a certain pair of protein atoms (or atom types) get inside a cut-off. How such a thing could arise might depend on how the force field does the parameter lookups. Imagine an exponent sign error on an LJ parameter on a pair of atom types unlikely to come into LJ contact... The nstxout/nstxtcout approach Justin and I suggest might allow you to see that kick happen before the nearby atoms get kicked again on the next time-step. 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] surface simulation
Hi, all gmx-users, I was simulating a CCl4 surface system. I encounter some problems. I hope for your help. First I built a 3x3x3 nm3 CCl4 box, then solved it into a 3x3x15 box in order to form gas/CCl4/gas surface system. After simulating in NVT, two CCl4 molecules run away to the gas phase. I want to know how to control CCl4 not to run to gas phase. I used the gromos96 force field. Can you help me? I expect your answer. Thanks a lot! H. Y. Xiao ___ 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] surface simulation
Hongyan Xiao wrote: Hi, all gmx-users, I was simulating a CCl_4 surface system. I encounter some problems. I hope for your help. First I built a 3x3x3 nm^3 CCl_4 box, then solved it into a 3x3x15 box in order to form gas/CCl4/gas surface system. After simulating in NVT, two CCl_4 molecules run away to the gas phase. I want to know how to control CCl_4 not to run to gas phase. I used the gromos96 force field. Can you help me? I don't follow. What's the gas? Anyhow, it seems your CCl_4 surface is sublimating, which might not be surprising. I expect your answer. Thanks a lot! I suspect this is just a language issue, but expect in English carries the implication that someone is obliged to make an answer. All of us here who might answer your email are volunteers. A paragraph like I'll look forward to any answers. Thanks a lot! will avoid annoying people :-) 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] CCl4 parameters problem
Hi, all gmx-users, I obtained the gromos96.1 itp file of CCl4 from the PRODRG program and I modified it to agree with the ffG53a6.itp force field parameters. Please see the following, [ moleculetype ] ; Name nrexcl CL4 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CLCL4 1 CL4 CL1 1 -0.062 35.4530 2 CCL4 1 CL4 CT 10.248 12.0110 3 CLCL4 1 CL4 CL4 1 -0.062 35.4530 4 CLCL4 1 CL4 CL2 1 -0.062 35.4530 5 CLCL4 1 CL4 CL3 1 -0.062 35.4530 [ bonds ] ; ai aj fuc0, c1, ... 2 1 20.176 810.00.176 810.0 ;CT CL1 2 3 20.176 810.00.176 810.0 ;CT CL4 2 4 20.176 810.00.176 810.0 ;CT CL2 2 5 20.176 810.00.176 810.0 ;CT CL3 [ pairs ] ; ai aj fuc0, c1, ... [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 2109.5 618.0109.5 618.0 ; CL1 CT CL4 1 2 4 2109.5 618.0109.5 618.0 ; CL1 CT CL2 1 2 5 2109.5 618.0109.5 618.0 ; CL1 CT CL3 3 2 4 2109.5 618.0109.5 618.0 ; CL4 CT CL2 3 2 5 2109.5 618.0109.5 618.0 ; CL4 CT CL3 4 2 5 2109.5 618.0109.5 618.0 ; CL2 CT CL3 [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... 2 1 3 4 2 35.3 334.8 35.3 334.8 ; impCT CL1 CL4 CL2 However, when I ran the grompp program, it pointed out the following the warning WARNING 1 [file ccl4.top, line 25]: Too few parameters on line (source file toppush.c, line 1499) I had a check the CCl4 parameters again and did not find the parameter lost. I want to know why the warning occurs? I hope for your help! Thanks! H. Y. Xiao ___ 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] CCl4 parameters problem
Hongyan Xiao wrote: Hi, all gmx-users, I obtained the gromos96.1 itp file of CCl_ 4 from the PRODRG program and I modified it to agree with the ffG53a6.itp force field parameters. Please see the following, [ moleculetype ] ; Name nrexcl CL4 3 [ atoms ] ;nr type resnr resid atom cgnr charge mass 1 CLCL4 1 CL4 CL1 1 -0.062 35.4530 2 CCL4 1 CL4 CT 10.248 12.0110 3 CLCL4 1 CL4 CL4 1 -0.062 35.4530 4 CLCL4 1 CL4 CL2 1 -0.062 35.4530 5 CLCL4 1 CL4 CL3 1 -0.062 35.4530 [ bonds ] ; ai aj fuc0, c1, ... 2 1 20.176 810.00.176 810.0 ;CT CL1 2 3 20.176 810.00.176 810.0 ;CT CL4 2 4 20.176 810.00.176 810.0 ;CT CL2 2 5 20.176 810.00.176 810.0 ;CT CL3 [ pairs ] ; ai aj fuc0, c1, ... [ angles ] ; ai aj ak fu c0, c1, ... 1 2 3 2109.5618.0109.5618.0 ; CL1 CT CL4 1 2 4 2109.5618.0109.5618.0 ; CL1 CT CL2 1 2 5 2109.5618.0109.5618.0 ; CL1 CT CL3 3 2 4 2109.5618.0109.5618.0 ; CL4 CT CL2 3 2 5 2109.5618.0109.5618.0 ; CL4 CT CL3 4 2 5 2109.5618.0109.5618.0 ; CL2 CT CL3 [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... 2 1 3 4 2 35.3 334.835.3 334.8 ; impCT CL1 CL4 CL2 However, when I ran the grompp program, it pointed out the following the warning WARNING 1 [file ccl4.top, line 25]: Too few parameters on line (source file toppush.c, line 1499) I had a check the CCl_4 parameters again and did not find the parameter lost. I want to know why the warning occurs? If you're working with the .top, what you've shown is not complete (at the very least, it is missing a call to #include ffG53a6.itp. What actually corresponds to line 25? What would the manual indicate about the contents of such a line? -Justin I hope for your help! Thanks! H. Y. Xiao ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://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] CCl4 parameters
Hi, Justin, This is my CCl4.top file. ; ; File 'ccl4.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Thu Oct 9 08:18:55 2008 ; ; This is your topology file ; God is a DJ (Faithless) ; ; Include forcefield parameters #include ffG53a6.itp #include ccl4.itp ; Include generic topology for ions #include ions.itp [ system ] ; Name Pure CL4 [ molecules ] ; Compound#mols CL4169 ~ What does it lose? Please give me further suggestion. Thanks again. H. Y. Xiao ___ 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] surface simulation
Hi, Mark Abraham, I accepted your suggestion on the language. I simulated the CCl4 surface system. In order to simplify model, using the vacuum replaced the gas phase. Furthermore, I found some paper by other people also deal with the gas/liquid using the vacuum. In vacuum/CCl4, can I control the CCl4 molecule not to run to the vacuum using the gromacs? For example, using the wall, but I do not set up wall parameters well. Please give me some suggestion. Thanks again! H. Y. Xiao ___ 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] ionic liquid
how to do molecular dynamics for ionic liquids by using GROMACS. Can u tell me the correct method to do molecular dynamics and which topologies are suitable for use with NMR-type calculations or all-atom force fields. ___ 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] email
[EMAIL PROTECTED] ___ 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] CCl4 parameters
I'll repeat my earlier question: What actually corresponds to line 25? What would the manual indicate about the contents of such a line? That is for you to tell us, so we don't have to sort through your topology. You have everything intact, including line spacing (which doesn't necessarily translate through email). If you can provide the exact line, what it contains, and which section of the topology of which it is a component (pairs, angles, dihedrals, etc) then maybe someone can provide useful advice. If you want free help, make it easy for us to help you. -Justin Hongyan Xiao wrote: Hi, Justin, This is my CCl4.top file. ; ; File 'ccl4.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Thu Oct 9 08:18:55 2008 ; ; This is your topology file ; God is a DJ (Faithless) ; ; Include forcefield parameters #include ffG53a6.itp #include ccl4.itp ; Include generic topology for ions #include ions.itp [ system ] ; Name Pure CL4 [ molecules ] ; Compound#mols CL4169 ~ What does it lose? Please give me further suggestion. Thanks again. H. Y. Xiao ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://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] help- ionic liquid
how to do molecular dynamics for ionic liquids by using GROMACS. Can u tell me the correct method to do molecular dynamics and which topologies are suitable for use with NMR-type calculations or all-atom force fields. ___ 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] surface simulation
Hongyan Xiao wrote: Hi, Mark Abraham, I accepted your suggestion on the language. I simulated the CCl_4 surface system. In order to simplify model, using the vacuum replaced the gas phase. Furthermore, I found some paper by other people also deal with the gas/liquid using the vacuum. In vacuum/CCl_4 , can I control the CCl_4 molecule not to run to the vacuum using the gromacs? For example, using the wall, but I do not set up wall parameters well. Please give me some suggestion. Thanks again! Some position restraints will keep your surface intact. See the manual for details. GROMACS will report how much energy is going from the restraints and you should check your parameterization by seeing that this energy is pretty small. 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] help- ionic liquid
naimah haron naimah wrote: how to do molecular dynamics for ionic liquids by using GROMACS. Can u tell me the correct method to do molecular dynamics and which topologies are suitable for use with NMR-type calculations or all-atom force fields. This question is too general for volunteers to help you with. Start with a Google search, some reading of the GROMACS manual, or doing some GROMACS tutorials. Then, if you need to, come back with focussed questions. 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] ready topology for ionic liquid?
how do i get the ready topology for ionic liquid?? ___ 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 lamboot
Hi everybody, I have question regarding parallel run. I am new to this and may sound very stupid so please bear with me. Our's is a 10.4.1 Mac Os X with 2 X 2.66 GHz Dual -Core Intel Xeon processor. Gromacs 3.3.1 was loaded in it. Then I had downloaded the lam-7.06 package from the gromacs homepage. The host file is present in /private/etc/ directory as expected and reads ## # Host Database # # localhost is used to configure the loopback interface # when the system is booting. Do not change this entry. ## 127.0.0.1 localhost 255.255.255.255 broadcasthost ::1 localhost However lamboot gives error on running on this host file. I want to know the correct way to modify the host file so that I can launch the lam/mpi environment. Any suggestion is welcome. Thanks in advance Sarbani ___ 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
