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

Hi Mark, On Sun, Nov 7, 2010 at 2:54 AM, Mark Abraham wrote: > 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. >> > > Aha, no

[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 sect

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

On 7/11/2010 8:02 PM, leila karami wrote: 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 a

[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 C

[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 befor

[gmx-users] (no subject)

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 Best wishes Mustafa MY EM.MDP integrator= steep nsteps=200 nstlist=10 rlist=1.0 coulombtype=pme rcoulomb=1.0 vdw_type=cut-off rvd

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 dumpe

[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 ps

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 wrote: From: atila petrosian Subject: [gmx-users] -b -e To: gmx-users@gromacs.org Date

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 HB2opl

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] -b -e

On 8/11/2010 12:01 AM, atila petrosian wrote: 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).

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 else'

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 http://lists.gromacs.org/mailman/listinfo/

Re: [gmx-users] gpu

tnx. Erik --- On Sun, 11/7/10, Rossen Apostolov wrote: From: Rossen Apostolov 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 On 11/7/10 1:23 PM

[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 complete

[gmx-users] Re: trjconv

Did you try to re-run your trajectory? Does the problem persist then? > 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 > >

Re: [gmx-users] Re: trjconv

Vitaly Chaban wrote: Did you try to re-run your trajectory? Does the problem persist then? Perhaps the faster solution would be to see what gmxcheck says about the trajectory. -Justin I have a trajectory with 2 frames. i want to separate just 1000 last frames of it in pdb formt an

[gmx-users] a bug in GMXRC.bash

Dear Gromacs developers, I noticed that the GMXRC.bash has been updated in gromacs 4.5.2, which leads to a wrong manipulation to the LD_LIBRARY_PATH variable. The leading colon is missing, when exporting this variable for the first time. 2010-11-08 Ye MEI -- gmx-users mailing listgmx

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

This was removed for security reasons. The leading colon adds the local directory to the list of directories searched for libraries. Why does your setup require the colon? Roland On Mon, Nov 8, 2010 at 2:04 AM, Ye MEI wrote: > Dear Gromacs developers, > > I noticed that the GMXRC.bash has been

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 bu

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 wrote: > > > Vitaly Chaban wrote: > >> Did you try to re-run your trajectory? Does the problem

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 sa