Re: [gmx-users] Run test in parallel

Dear Yang, Thank you for your corporation. Regards, Teru 2008/8/7 Yang Ye <[EMAIL PROTECTED]>: > ikedaike wrote: >> >> Dear Yang, >> >> Thank you for your quick reply. >> >> I checked the log files and then found that the mpirun command cannot >> find the mdrun(executable) file.. >> I modified t

Re: [gmx-users] Run test in parallel

ikedaike wrote: Dear Yang, Thank you for your quick reply. I checked the log files and then found that the mpirun command cannot find the mdrun(executable) file.. I modified to use the absolute path in the gmxtest.pl and ran it. However some tests still failed. % ./gmxtest.pl -np 8 all Will te

Re: [gmx-users] Run test in parallel

Dear Yang, Thank you for your quick reply. I checked the log files and then found that the mpirun command cannot find the mdrun(executable) file.. I modified to use the absolute path in the gmxtest.pl and ran it. However some tests still failed. % ./gmxtest.pl -np 8 all Will test on 8 processors

Re: [gmx-users] Run test in parallel

I would guess that you have got gromacs installed correctly from the two-process tests. The failure of eight-core test may depends how you start your MPI daemon or other factors that mdrun could be not running at all. Paste your log file from eight-core test or just wait for some one has experien

[gmx-users] nature of gromacs / gcc-4.x problem

Hello, I am trying to track down the exact nature of the gcc-4.1.x / gromacs bug. I have a system on which we were forced to reinstall gromacs (3.3.1 and 3.3.3) about 2 weeks ago and I didn't realize that the default gcc was bumped to 4.1.2. I am interested because ideally we won't need t

[gmx-users] Run test in parallel

Hi I built GROMACS-3.3.3 with GCC-3.4.6 and OpenMPI-1.2.5 on CentOS 4.5(Intel Core2 Duo). I tested with gmxtest-3.3.3 and all tests passed in non-parallel. However, when I tested in parallel, I encountered the following messages. [Use 2 Cores] % ./gmxtest.pl -np 2 all Will test on 2 processors Al

Re: [gmx-users] remove center of mass motion

M. Emal Alekozai wrote: Dear All, I have a trajectory where the center of mass motion is not removed. In the mdrun.mdp file the option "comm-grps" was commented out: ; mode for center of mass motion removal = comm-mode= Linear ; number of steps for center of mass mot

[gmx-users] gromos function type assigned by grompp

Hi I am trying to set a calculation based on the GROMOS force field in a program I have and I am using GROMACS to generate the (starting) input files for me. From reading the manual I know that GROMOS uses a fourth power potential (type 2) for bonds and a cosine based angle potential (type 2), bu

Re: [gmx-users] top file definitions_1

[EMAIL PROTECTED] wrote: Dear Community, I am trying to manually define a .top file of an organic molecule (a modified bisphosphonate). I am not a gromacs user but a lab mate is, so he will make the run. It has been several days since I started to search for a text where the .top format is

[gmx-users] top file definitions_1

Dear Community, I am trying to manually define a .top file of an organic molecule (a modified bisphosphonate). I am not a gromacs user but a lab mate is, so he will make the run. It has been several days since I started to search for a text where the .top format is depicted in detail but the o

[gmx-users] remove center of mass motion

Dear All, I have a trajectory where the center of mass motion is not removed. In the mdrun.mdp file the option "comm-grps" was commented out: ; mode for center of mass motion removal = comm-mode= Linear ; number of steps for center of mass motion removal = nstcomm

[gmx-users] Determining temperature from velocities

I was wondering how g_energy determines the temperature of the groups. I am trying to measure temperature based upon distance from a point radially outward. To implement I thought about writing a code to input the final velocities to determine average temperature based upon a central point. Thanks

[gmx-users] peptide translation

Dear All, I have a lipid - peptide system and while running the production run I forgot to assign comm-grps, thus the peptide has actually shifted from the center towards one of the edges. I have searched the forum and tried all possible options in trjconv i.e. -center zero, -fit translation, p

Re: [gmx-users] membrane with OPLS force field

Volker Wirth wrote: Hi Justin, thanks a lot for your response! Of course my mail was a bit "provocative", as I know that combination methods are state of the art, used in many publications and leading to reasonable results. (time scale eight months). Combining different force fields (Berger/

Re: [gmx-users] Some Issues on Substrates/PBC

André Farias de Moura wrote: Hi Michael, if you are not interested in the substrate dynamics, then you could try the freeze group options (freezegrps and freezedim). I have used these options for graphite and it worked just fine. best, André In addition to that, you may consider using pbc =

Re: [gmx-users] Some Issues on Substrates/PBC

Hi Michael, if you are not interested in the substrate dynamics, then you could try the freeze group options (freezegrps and freezedim). I have used these options for graphite and it worked just fine. best, André > Dear Listmembers, > > This post is quite lengthy because it contains several diffe

Re: [gmx-users] membrane with OPLS force field

Hi Justin, thanks a lot for your response! Of course my mail was a bit "provocative", as I know that combination methods are state of the art, used in many publications and leading to reasonable results. >> (time scale eight months). Combining different force fields >> (Berger/GROMOS, Berger/OPLS

[gmx-users] Some Issues on Substrates/PBC

Dear Listmembers, This post is quite lengthy because it contains several different problems that I came across during my simulations and that I cannot figure out up to now. I included some links to pictures to give you some visualization and would be glad for every suggestion or hint even to part

Re: [gmx-users] membrane with OPLS force field

Volker Wirth wrote: standard acyl chain parameters fail when they get too long. I think there ref. for that is a Berendsen paper on hexadecane simulations, but I could be wrong there. In any event, 'protein' parameters do not appear to transfer directly to long acyl chains in a simple way and t

[gmx-users] RE[4]: Define proper set of topology parameters for new molecule in different FF.

>>I want to construct TOPOLOGY of many different molecules using different >>Force Fields (FF). >> >>If i want to describe , for example, METHYL ACETATE in OPLS-AA force field >> >> O Hc5 >> || | >> C---O1C2Hc4 >> |

[gmx-users] how to fix the center of mass of the protein in the pull simulation

Dear users: how to fix the center of mass of the protein in the pull simulation? I want to know to know! Please help me! - 雅虎邮箱，您的终生邮箱！___ gmx-users mailing listgmx-users@gromacs.org http://www.groma

[gmx-users] RE: how to fix the COM of group in the pull.

>Dear users: >I want to know how to fix the com of the group in the pull or afm simulation,Please give some ideas. comm-grps in grompp.mdp, isn't it? -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq., 4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vv

Re: [gmx-users] membrane with OPLS force field

> standard acyl chain parameters fail when they get too long. I think there > ref. for that is a Berendsen paper on hexadecane simulations, but I could be > wrong there. In any event, 'protein' parameters do not appear to > transfer directly to long acyl chains in a simple way and therefore your >

[gmx-users] A fix to eigio.c ?

make_edi crashes on 3.3.3 (but not on 3.3.1). I think the problem is in eigio.c where the following lines were added after 3.3.1: eignr=NULL; eigval=NULL; eigvec=NULL; I guess it should be: *eignr=NULL; *eigval=NULL; *eigvec=NULL; Elad P. __