Re: [gmx-users] Using mdrun -rerun to get energy values

Hi Mark, On Sun, Nov 7, 2010 at 2:54 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 7/11/2010 4:14 AM, Martin Kamp Jensen wrote: Hi Chris, On Sat, Nov 6, 2010 at 5:58 PM, Krzysztof Mlynarczyk mitomas...@gmail.com wrote: Hi, You need to use md integrator for -rerun to work.

[gmx-users] kind of contacts in protein-dna interaction during simulation

Hi gromacs users In following article, in table 2, author brings Protein–DNA contacts observed in the simulation. I want to know how to obtain 1) Van der Waals interactions 2) percentage of population regarding Direct hydrogen bond, Van der Waals and Water-mediated hydrogen bond. In method

[gmx-users] kind of contacts in protein-dna interaction during simulation

Dear Mark thanks for your attention. I read manual before. I know that g_hbond is for hydrogen bond analysis. But I don’t know about Van der Waals interactions analysis and how to obtain percentage of them. Please give me more information about what I said. -- Leila Karami Ph.D. student of

[gmx-users] add a group to an amino acid

Hi, I'm using the OPLS force field. [ PHE ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B 0.140 1 HAopls_1400.060 1 CBopls_149 -0.005 2 HB1opls_1400.060 2 HB2opls_1400.060 2

[gmx-users] gpu

Dear gmx-users, How to invoke the gpu for simulations, e.g. is there (compiler) flag? Cheers, Erik -- 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

Re: [gmx-users] problem in executing genbox command

On 06/11/10 07:46, Mark Abraham wrote: On 6/11/2010 4:02 PM, bharat gupta wrote: Hi all , Whenever i am running the genbox command I am getting the following error :- genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top :-) G R O M A C S (-: Segmentation fault (core

[gmx-users] -b -e

Dear gromacs users my simulation time is 10 ns (1 ps), but, I want to use last 4ns for analysis. for example, if I use g_rms -b 6000 -e 1 -o rmsd.xvg, in xvg output file, rmsd plotted versus time (from 6000 to 1 ps in horizontal axis). while I want horizontal axis be from 0 to 4000

Re: [gmx-users] -b -e

Hi Atila,  You can use gmxtool trjconv to create a new trajectory file of the last 4ns. Or consider grace (obtain from the net) to modify the axis of your plot by hand. --- On Sun, 11/7/10, atila petrosian atila.petros...@gmail.com wrote: From: atila petrosian atila.petros...@gmail.com

Re: [gmx-users] add a group to an amino acid

hengame fallah wrote: Hi, I'm using the OPLS force field. [ PHE ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B 0.140 1 HAopls_1400.060 1 CBopls_149 -0.005 2 HB1opls_1400.060 2 HB2

Re: [gmx-users] (no subject)

mustafa bilsel wrote: Hi, when I tried to make energy minimisation, I see following error. My parameters are at the end of the email. What should I do? Fatal error: Atomtype HW not found More pertinent information would be a description of your system, which force field you're using, as

Re: [gmx-users] kind of contacts in protein-dna interaction during simulation

On 7/11/2010 9:36 PM, leila karami wrote: Dear Mark thanks for your attention. I read manual before. I know that g_hbond is for hydrogen bond analysis. But I don’t know about Van der Waals interactions analysis and how to obtain percentage of them. If you're planning to copy someone

Re: [gmx-users] gpu

Hi, Did you read this? http://www.gromacs.org/gpu Rossen On 11/7/10 1:23 PM, Erik Wensink wrote: Dear gmx-users, How to invoke the gpu for simulations, e.g. is there (compiler) flag? Cheers, Erik -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] gpu

tnx. Erik --- On Sun, 11/7/10, Rossen Apostolov ros...@kth.se wrote: From: Rossen Apostolov ros...@kth.se Subject: Re: [gmx-users] gpu To: gmx-users@gromacs.org Date: Sunday, November 7, 2010, 4:27 PM Hi, Did you read this? http://www.gromacs.org/gpu Rossen

[gmx-users] trjconv

Dear Gro.users I have a trajectory with 2 frames. i want to separate just 1000 last frames of it in pdb formt and 1000 first frames too. I entered this command: trjconv -f mmm.trr -o nnn.pdb -s lll.tpr -b 800 -e 1000 actually my total time is 1000 ps. the process was not done

Re: Re: [gmx-users] a bug in GMXRC.bash

But later LD_LIBRARY_PATH is redefined as LD_LIBRARY_PATH=${GMXLDLIB}${LD_LIBRARY_PATH} without a colon between ${GMXLDLIB} and ${LD_LIBRARY_PATH} Ye MEI 2010-11-08 From: Roland Schulz Date: 2010-11-08 15:31:24 To: Discussion list for GROMACS users CC: Subject: Re: [gmx-users] a

Re: [gmx-users] Re: trjconv

Dear justin I checked what you said,yes,both of them(trr and xtc files) were completely done as I wanted in my mdp file. what is your points of view? On Sun, Nov 7, 2010 at 9:15 PM, Justin A. Lemkul jalem...@vt.edu wrote: Vitaly Chaban wrote: Did you try to re-run your trajectory? Does

Re: [gmx-users] Re: trjconv

of course I could generate a pdb file without -b and -e options,but I don't want it. besides I did the same process with xtc file and I resulted in a 0 byte file :( On Mon, Nov 8, 2010 at 11:21 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear justin I checked what you