Re: [gmx-users] Force vs distance plot in pulling simulation?
16 nov 2012 kl. 22.42 skrev Justin Lemkul: On 11/16/12 10:45 AM, Gmx QA wrote: Hello gmx-users, I've performed a pulling simulation and obtained a force-vs-time plot and a distance-vs-time plot (xvg-files). Is it common to somehow combine these to get a force-vs-distance-plot using a hacked-together script, or how do people that have experience with pulling generally make such a plot? I have read a bunch of papers where such figures are presented, but there does not seem to be any built-in way in gromacs to make them. I could be wrong, of course. The only solution is to write a simple script that parses out the columns you want. -Justin I don't see the point though. Except for checking implementation of the pull code. --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Pull code, Velocity distribution
Hello, Sorry for bothering you with the same question but just want to make sure that I am getting my results correctly. I run simulations where two blocks of ice are in a sliding contact for 5 ns (using pull code). As an output of the simulation I have pullf.xvg file which I use for 'g_analyze -f pullf.xvg' command and assume that the average force it prints is the average pulling force calculated with the U = 1/2K(vt-(x-x0))^2 harmonic potential. Sorry again for double checking! Cheers, Nino From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Friday, November 02, 2012 5:04 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Pull code, Velocity distribution On 11/2/12 10:52 AM, Samadashvili Nino wrote: Hello, I have been using the pull code for friction calculations. I am not doing umbrella sampling but just pulling one slab of crystal on top of another with the constant velocity. I would like to know how Gromacs is calculating the pulling force (pullf.xvg) during sliding. Is the pulling force obtained through U = 1/2K(vt-(x-x0))^2 harmonic potential? This should be correct. I am using following parameters: pull = umbrella pull_geometry= direction_periodic pull_dim= Y Y Y pull_start = yes pull_ngroups = 1 pull_group0= ICE_A pull_group1= ICE_B pull_pbcatom0 = 0 pull_pbcatom1 = 0 pull_vec1 = 1 0 0 pull_rate1 = 0.004 pull_k1 = 1 Since I have pull_start=yes, does it mean that the initial spring length is the COM distance between ICE_A and ICE_B? Yes. Another question is regarded to the velocity distribution. I used g_traj to plot the velocity distribution of my system which I compared with the distribution plot calculated from the coordinates and they dont match. The distribution calculated by Gromacs has a tail while my calculations don't show any. Could you please tell me how is it calculated in Gromacs? How what is calculated? How are you creating your own distributions from the coordinates? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Force vs distance plot in pulling simulation?
Hi Erik and Justin Thanks, writing such a script is easy. The point of it all would be to be able to map the magnitude of the pulling force to what I see happen in the pulling simulation. How else would you get an understanding of what the pulling force means? Thanks /PK The only solution is to write a simple script that parses out the columns you want. -Justin I don't see the point though. Except for checking implementation of the pull code. --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se javascript:; http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org javascript:; http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org javascript:;. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus
Hi all. After using amber03 force field for protein-ligand simulation (pdb2gmx), I encountered with following error: Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus. Ligand in my system is a single residue (GLN). There are [GLN], [NGLN] and [CGLN] in rtp file of amber03 force field. Should this single residue be as both of [NGLN] and [CGLN]? How to fix this error? Any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus
On 2012-11-17 15:37, Atila Petrosian wrote: Hi all. After using amber03 force field for protein-ligand simulation (pdb2gmx), I encountered with following error: Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus. Ligand in my system is a single residue (GLN). There are [GLN], [NGLN] and [CGLN] in rtp file of amber03 force field. Should this single residue be as both of [NGLN] and [CGLN]? How to fix this error? Any help will highly appreciated. Manually making a toplogy is your best best. Add an alanine after the gln then in the top file rename and remove atoms. GAFF is an alternative but it will not give you exactly the same charges and LJ parameters. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] simulation with two different force fields
On 11/17/12 10:19 AM, shahab shariati wrote: Dear gromacs users Can I use two different force fields for a system with 2 components (dna and carbon nano tube)? No. Mixing and matching force fields (even if syntactically possible in the topology) invalidates the force field models. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] simulation with two different force fields
On 11/17/12 10:37 AM, shahab shariati wrote: Dear Justin Thanks for your attention. You are right but is there a force field which be appropriate for both of protein and carbon nano tube or dna and carbon nano tube? What does your search of the literature tell you? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus
On 2012-11-17 16:26, Atila Petrosian wrote: Dear David Thanks for your quick reply. You said Add an alanine after the gln then in the top file rename and remove atoms. I confused. Why ALA? ALA (alanine) is a residue which is very simple than GLN structurally. I should add alanine after the gln. But in which file? you make a separate molecule Gln-Ala using pymol or vmd and then run it through pdb2gmx, this will give you NGLN-CALA. Then you edit the top file (remove superfluous alanine atoms, rename the N in ALA to O2 etc) with a text editor until it is correct with help from the rtp file for CGLN. You may have to smooth the charges to keep it neutral. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] (no subject)
-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
