Re: [gmx-users] mass changes in free energy calculations
Thanks for clearing the doubt. Is that more easier to get equlibrium to use unchanged mass when doing LJ turning on/off? I ask this since I found the forwards and backwards mutation free energy are more consistant if I do not change the mass. Accidentally? LQ On Thu, Jun 19, 2008 at 4:26 AM, David Mobley <[EMAIL PROTECTED]> wrote: > You can change the mass if you like. Basically, the net free energy > change associated with changing the mass should end up being zero so > it will be irrelevant. The mass of course affects the dynamics and > things like the velocities, but based on equipartition you can > convince yourself that the free energy change will be zero. > > David > > On Fri, Jun 13, 2008 at 12:04 AM, friendli <[EMAIL PROTECTED]> wrote: > > Dear all, > > > > I am calculating FE using TI. I have a question about mutating existing > > atoms with different mass. > > for example, using ffG53a6 force field, in one case i need to mutate CH2 > to > > CH3, > > should I use > > [ atoms ] > > 17CH3 2ALA CB 6 0 15.035 CH2 > 0 > >14.027; qtot 1 > > > > OR > > > > 17CH3 2ALA CB 6 0 15.035 CH2 > 0 > >15.035; qtot 1 > > > > I notice from Prof. Alan Mark's online FE course, he mutates a H atom to > a O > > atom, but does not change its mass. > > The line is : > > 12HC1 PHE HZ 6 0.11.008 > > OA -0.54811.008 > > > > Can somebody explain a bit why we should not change the mass accordingly? > > > > > > thank you > > > > LQ > > > > I though I sent this email but why I can not see it. There may be > something > > wrong with my email software. so I send here again. sorry > > ___ > > 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 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] Low CPU usage multicore
Justin A. Lemkul wrote: When asking for free help, make it easy on those from whom you seek it. Pertinent information would include: 1. Gromacs version 2. MPI implementation you are using (OpenMPI, lam, etc.) 3. Hardware details 4. MPI host configuration 5. GROMACS command lines you're using. Otherwise, we're left to assume that you've simply done something wrong, and that's certainly not useful to anyone. Agreed. 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] [Fwd: Installation Doubt]
Please put GROMACS-related correspondence on the list. That way multiple people can have a chance to reply, and the answer is archived for all to search. There are instructions that pertain to the installation of a suitable FFTW here http://www.gromacs.org/content/view/23/33/ Please read them. Mark Original Message Subject:Installation Doubt Date: Fri, 20 Jun 2008 12:10:23 -0700 (PDT) From: abhijit ramachandran <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] Hi Mark, I was going through the forums and saw your replies the most so decided to ask you a general basic question, i am trying to install Gromac3.3 onto a Linux PC and it had a pre-req for FFTW installation so i installed FFTW on it but when i give the ./configure command for installing the Gromac it gives me an error stating that "Cannot to find fftw3f library file" and so it doesnt continue with remaining installation, so my question is have i installed FFTW properly and is there any way i can check it, if yes then what am i doing wrong that it gives me an error. Please reply since i am just begining to use it. Innconvinience caused is regretted. Regards Abhijit R ___ 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] Low CPU usage multicore
When asking for free help, make it easy on those from whom you seek it. Pertinent information would include: 1. Gromacs version 2. MPI implementation you are using (OpenMPI, lam, etc.) 3. Hardware details Otherwise, we're left to assume that you've simply done something wrong, and that's certainly not useful to anyone. -Justin ha salem wrote: Dear Users my multi-core cpus usage are low in parallel run,when I run on 1 cpu all of core have 90% usage but when I run on 2 nodes (every one has 1 multicore cpu) the cpu usage is low its about 2 month I cant solve this problem thank you ___ 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] Low CPU usage multicore
Dear Users my multi-core cpus usage are low in parallel run,when I run on 1 cpu all of core have 90% usage but when I run on 2 nodes (every one has 1 multicore cpu) the cpu usage is low its about 2 month I cant solve this problem thank you ___ 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] mdp files
You have to make it with a text editor. -Justin [EMAIL PROTECTED] wrote: Special thanks to Vitaly, Mark and Justin for there comments. I've revisited the wiki site and read through chapter 5 of the manual. I'm currently going through the tutorial with a standard protein. I run into a problem when I use the command: grompp -f em.mdp -c fws_b4em.pdb -p fws.top -o fws_em.tpr The error states that the em.mdp file doesn't exists, but none of the steps in the tutorial leading up to this command creates the em.mdp file. I was just wondering what step in the process is the .mdp file created or do I have to have that already created off to the side ready for the grompp command? Thanks again, -John Landers ___ 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] mdp files
Special thanks to Vitaly, Mark and Justin for there comments. I've revisited the wiki site and read through chapter 5 of the manual. I'm currently going through the tutorial with a standard protein. I run into a problem when I use the command: grompp -f em.mdp -c fws_b4em.pdb -p fws.top -o fws_em.tpr The error states that the em.mdp file doesn't exists, but none of the steps in the tutorial leading up to this command creates the em.mdp file. I was just wondering what step in the process is the .mdp file created or do I have to have that already created off to the side ready for the grompp command? Thanks again, -John Landers ___ 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: msd vs. time plot for molecules
> Using g_msd on a group of atoms results in an msd vs. time plot which is > the result of an average over all the atoms' motions. I would like to > obtain the same plot, but for an average over the center of mass motions > of a group of molecules. Using the -mol option results in a plot of the > diffusion coefficient for each individual molecule. Do I need to use > the -mw option for each molecule seperately and then average them > together myself? Thank you for any ideas. It seems that because MSDs of separate atoms are mostly very close to those of the center-of-mass GROMACS developers has made the latter case default. Using the '-mol' of g_msd option should give you a diffusion constant of the center-of-mass (besides that graph)... I'm not sure, however. It's also a good idea to examine a programme code. :) -- Vitaly V. Chaban School of Chemistry University of Kharkiv Svobody sq.,4 Kharkiv 61077, Ukraine ___ 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] MPICH2 and parallel Gromacs errors
Hi Richard, I don't know about Gromacs specifically, but our users have had more luck getting MPI functionality for our software on Mac clusters/multi- core computers with OpenMPI. Cheers, - Art. On Jun 20, 2008, at 9:43 AM, Casey,Richard wrote: Hello, This issue appears to have been encountered by many people. We've searched the discussion archives and tried every recommended solution but no luck. We have MPICH2 v.1.0.7 installed on an Apple G5 cluster (64 CPU's). And installed Gromacs v.3.3.3 with --enable-mpi option. Single CPU jobs run OK; parallel jobs always fail. For parallel jobs we use: grompp -v -np 2 -p topol.top (or other values for np for more cpu's) We launch MPD with: mpdboot -n 2 -f /common/mpich2/mpd.hosts We run jobs with: /common/mpich2/bin/mpiexec -l -n 2 \ /common/gromacs/bin/mdrun_mpi -v -np 2 \ -s /Users/richardcasey/topol.tpr \ -g /Users/richardcasey/md.log \ -e /Users/richardcasey/ener.edr \ -o /Users/richardcasey/traj.trr \ -x /Users/richardcasey/traj.xtc \ -c /Users/richardcasey/confout.gro The output always says: --- 1: Program mdrun_mpi, VERSION 3.3.3 1: Source code file: init.c, line: 69 1: 1: Fatal error: 1: run input file /Users/richardcasey/topol.tpr was made for 2 nodes, 1: p0_29762: p4_error: : -1 1: while mdrun_mpi expected it to be for 1 nodes. 1: --- We've tried everything (many variations on the above and recommendations from the discussion list) but for some reason mdrun_mpi insists that it use a single-cpu version of the topology file. We've check environment variables and they appear to point to the right directories. /common is NFS mounted on all nodes. Completely stumped - no idea what is wrong here. Any suggestions? Richard Casey ___ 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 ___, Dr. Art FY Poon __/ `–– Division of Comparative Pathology and Medicine ___/ \ Department of Pathology \___ University of California, San Diego ___ 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] msd vs. time plot for molecules
Using g_msd on a group of atoms results in an msd vs. time plot which is the result of an average over all the atoms' motions. I would like to obtain the same plot, but for an average over the center of mass motions of a group of molecules. Using the -mol option results in a plot of the diffusion coefficient for each individual molecule. Do I need to use the -mw option for each molecule seperately and then average them together myself? Thank you for any ideas. --Mike Skaug ___ 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: modelling a new molecule in OPLS
Anandita, Just to add my response on the pile (and do take the previous advice) what you show here displays a problem of yours with respect to molecular dynamics simulations. That naming should be consistent, sure, if you know what you're doing you can sort of ignore warnings like 'atom names don't match (ABC1 - 1ABC)'. But the warnings about bond/angle/dihedral defaults and using zeroes. If one thinks to do standard stuff and stumbles upon one of these, sure, we'll help, and we did (check the archives). But if you're doing your own calculations for a force field and then come up with this... Now working on a force field, at least you should be natively aware that a bond definition requires two atoms and a bond length (and possibly a force constant). An angle is not created by simply listing three atoms. You need an angle! Likewise for a dihedral. You should probably spend some (more) time reading chapters 4 and 5 of the manual. Cheers, Tsjerk On Fri, Jun 20, 2008 at 3:53 PM, Vitaly Chaban <[EMAIL PROTECTED]> wrote: >> I have built an all atom topology file for "chaps" as i have already >> discussed in previous mails, with charges from Gaussian DFT. The current >> problem is with the grompp. > I think you should at least consult the existing examples of force > fields. > > Also, everybody here will be very happy if you not send so lengthy messages to > the list. There's no sense to cite all errors the programme displays. > > -- > Vitaly V. Chaban > > ___ > 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] topology for c-alpha protein model
After pdb2gmx of the whole structure, make an index file and them run another pdb2gmx choosing the c-alpha group. I hope it helps. 2008/6/20, Lillian Chong <[EMAIL PROTECTED]>: > > Dear Gromacs Users, > > I would like to generate a topology for a protein in which each > residue is represented only by its C-alpha atom (a Go-type model). > What would be the most straightforward way of creating this topology > file? > > Thanks in advance, > Lillian > ___ > 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] MPICH2 and parallel Gromacs errors
Hello, This issue appears to have been encountered by many people. We've searched the discussion archives and tried every recommended solution but no luck. We have MPICH2 v.1.0.7 installed on an Apple G5 cluster (64 CPU's). And installed Gromacs v.3.3.3 with --enable-mpi option. Single CPU jobs run OK; parallel jobs always fail. For parallel jobs we use: grompp -v -np 2 -p topol.top (or other values for np for more cpu's) We launch MPD with: mpdboot -n 2 -f /common/mpich2/mpd.hosts We run jobs with: /common/mpich2/bin/mpiexec -l -n 2 \ /common/gromacs/bin/mdrun_mpi -v -np 2 \ -s /Users/richardcasey/topol.tpr \ -g /Users/richardcasey/md.log \ -e /Users/richardcasey/ener.edr \ -o /Users/richardcasey/traj.trr \ -x /Users/richardcasey/traj.xtc \ -c /Users/richardcasey/confout.gro The output always says: --- 1: Program mdrun_mpi, VERSION 3.3.3 1: Source code file: init.c, line: 69 1: 1: Fatal error: 1: run input file /Users/richardcasey/topol.tpr was made for 2 nodes, 1: p0_29762: p4_error: : -1 1: while mdrun_mpi expected it to be for 1 nodes. 1: --- We've tried everything (many variations on the above and recommendations from the discussion list) but for some reason mdrun_mpi insists that it use a single-cpu version of the topology file. We've check environment variables and they appear to point to the right directories. /common is NFS mounted on all nodes. Completely stumped - no idea what is wrong here. Any suggestions? Richard Casey ___ 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] topology for c-alpha protein model
Dear Gromacs Users, I would like to generate a topology for a protein in which each residue is represented only by its C-alpha atom (a Go-type model). What would be the most straightforward way of creating this topology file? Thanks in advance, Lillian ___ 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: modelling a new molecule in OPLS
> I have built an all atom topology file for "chaps" as i have already > discussed in previous mails, with charges from Gaussian DFT. The current > problem is with the grompp. I think you should at least consult the existing examples of force fields. Also, everybody here will be very happy if you not send so lengthy messages to the list. There's no sense to cite all errors the programme displays. -- Vitaly V. Chaban ___ 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] modelling a new molecule in OPLS
When asking for free help, it is often best to make life easy on those from whom you're requesting it :-) I don't know if anyone on this list is going to take the time to hunt through hundreds of lines of your topology, identify the atom numbers involved in your errors, determine which atoms those numbers correspond to, and try to figure out what your problem is. That said, there is some general advice that I will give. If grompp cannot find default parameters for a given set of atoms (for any item - bonds, angles, dihedrals, etc.) it is because they are not present in the original force field. That means you either made a mistake in defining atom types or the numbering of the topology, or you will have to come up with the parameters for that item yourself. -Justin ANINDITA GAYEN wrote: I have built an all atom topology file for "chaps" as i have already discussed in previous mails, with charges from Gaussian DFT. The current problem is with the grompp. The error results that: processing topology... Generated 342378 of the 342378 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 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] modelling a new molecule in OPLS
I have built an all atom topology file for "chaps" as i have already discussed in previous mails, with charges from Gaussian DFT. The current problem is with the grompp. The error results that: processing topology... Generated 342378 of the 342378 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 342288 of the 342378 1-4 parameter combinations WARNING 1 [file "now1opls.itp", line 317]: No default Bond types, using zeroes WARNING 2 [file "now1opls.itp", line 320]: No default Bond types, using zeroes WARNING 3 [file "now1opls.itp", line 321]: No default Bond types, using zeroes WARNING 4 [file "now1opls.itp", line 322]: No default Bond types, using zeroes WARNING 5 [file "now1opls.itp", line 323]: No default Bond types, using zeroes WARNING 6 [file "now1opls.itp", line 324]: No default Bond types, using zeroes WARNING 7 [file "now1opls.itp", line 325]: No default Bond types, using zeroes WARNING 8 [file "now1opls.itp", line 326]: No default Bond types, using zeroes WARNING 9 [file "now1opls.itp", line 486]: No default Angle types, using zeroes WARNING 10 [file "now1opls.itp", line 487]: No default Angle types, using zeroes WARNING 11 [file "now1opls.itp", line 488]: No default Angle types, using zeroes WARNING 12 [file "now1opls.itp", line 489]: No default Angle types, using zeroes WARNING 13 [file "now1opls.itp", line 490]: No default Angle types, using zeroes WARNING 14 [file "now1opls.itp", line 491]: No default Angle types, using zeroes WARNING 15 [file "now1opls.itp", line 492]: No default Angle types, using zeroes WARNING 16 [file "now1opls.itp", line 607]: No default Angle types, using zeroes WARNING 17 [file "now1opls.itp", line 608]: No default Angle types, using zeroes WARNING 18 [file "now1opls.itp", line 612]: No default Improper Dih. types, using zeroes WARNING 19 [file "now1opls.itp", line 613]: No default Improper Dih. types, using zeroes WARNING 20 [file "now1opls.itp", line 614]: No default Improper Dih. types, using zeroes WARNING 21 [file "now1opls.itp", line 615]: No default Improper Dih. types, using zeroes WARNING 22 [file "now1opls.itp", line 616]: No default Improper Dih. types, using zeroes WARNING 23 [file "now1opls.itp", line 617]: No default Improper Dih. types, using zeroes WARNING 24 [file "now1opls.itp", line 618]: No default Improper Dih. types, using zeroes WARNING 25 [file "now1opls.itp", line 619]: No default Improper Dih. types, using zeroes WARNING 26 [file "now1opls.itp", line 620]: No default Improper Dih. types, using zeroes WARNING 27 [file "now1opls.itp", line 621]: No default Improper Dih. types, using zeroes WARNING 28 [file "now1opls.itp", line 622]: No default Improper Dih. types, using zeroes WARNING 29 [file "now1opls.itp", line 623]: No default Improper Dih. types, using zeroes WARNING 30 [file "now1opls.itp", line 624]: No default Improper Dih. types, using zeroes WARNING 31 [file "now1opls.itp", line 625]: No default Improper Dih. types, using zeroes WARNING 32 [file "now1opls.itp", line 626]: No default Improper Dih. types, using zeroes WARNING 33 [file "now1opls.itp", line 627]: No default Improper Dih. types, using zeroes WARNING 34 [file "now1opls.itp", line 628]: No default Improper Dih. types, using zeroes WARNING 35 [file "now1opls.itp", line 629]: No default Improper Dih. types, using zeroes WARNING 36 [file "now1opls.itp", line 630]: No default Improper Dih. types, using zeroes WARNING 37 [file "now1opls.itp", line 631]: No default Improper Dih. types, using zeroes WARNING 38 [file "now1opls.itp", line 632]: No default Improper Dih. types, using zeroes WARNING 39 [file "now1opls.itp", line 633]: No default Improper Dih. types, using zeroes WARNING 40 [file "now1opls.itp", line 634]: No default Improper Dih. types, using zeroes WARNING 41 [file "now1opls.itp", line 635]: No default Improper Dih. types, using zeroes WARNING 42 [file "now1opls.itp", line 636]: No default Improper Dih. types, using zeroes WARNING 43 [file "now1opls.itp", line 637]: No default Improper Dih. types, using zeroes WARNING 44 [file "now1opls.itp", line 638]: No default Improper Dih. types, using zeroes WARNING 45 [file "now1opls.itp", line 639]: No default Improper Dih. types, using zeroes WARNING 46 [file "now1opls.itp", line 640]: No default Improper Dih. types, using zeroes WARNING 47 [file "now1opls.itp", line 641]: No default Improper Dih. types, using zeroes WARNING 48 [file "now1opls.itp", line 642]: No default Improper Dih. types, using zeroes WARNING 49 [file "now1opls.itp", line 643]: No default Improper Dih. types, using zeroes WARNING 50 [file "now1opls.itp", line 644]: No default Improper Dih. types, using zeroes WARNING 51 [file "now1opls.itp", line 645]: No default Improper Dih. types, using zeroes WARNING 52 [file "now1opls.itp", line 646]: No default Improper Dih. types, using zeroes WARNING 53 [file "now1opls.itp", line 6
Re: [gmx-users] Carbon Nanotube Residue
> I'm new to gromacs and the past week or so I've been digging through the > archives so that I can simulate a carbon nanotube. I've been able find > coordinates for the carbon nanotube as well as the parameters for the > force field. My question is: > > Do I define the parameters in the force field file or can I do it in pdb > file? > > I'm asking because I'm unable to change the force field file, so if I > could just define the carbon nano tube residue in the pdb file that would > help me out a lot. See also http://www.gromacs.org/component/option,com_docman/task,doc_details/gid,100/Itemid,26/ for reference what the topology should like like. For some time, I was working with the problem of simulating the CNT by means of GROMACS, and I'll be glad to consult you if you have got any additional questions. Best, Vitaly ___ 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
