Re: [gmx-users] Benchs on gcc and pgi

Hi, On May 18, 2006, at 11:47 PM, Not wanting to press on this subject, that from previous discussions in this list seems to be a somewhat "sensible" one: You mean that the only and last thing that still need/should be "converted" to make Gromacs run on GPUs (or somehow slacing the job

Re: [gmx-users] Question about Athlon 64 4800+ x2 (poor performance)

gromacs3 wrote: Dear users I compiled Gromacs-3.3.1 from the src-rpm, on my system x86_64 FC5 (Athlon 64 4800+ x2, 4Gb DDR). When I tested gromacs over one of my molecular system I noticed its very poor performance. please give numbers. did you use MPI to use the two cores? Can anybody t

[gmx-users] CHARMM force field - contribution???

Hi there everybody, I have noticed in some previous mailings a discussion of implementation of the CHARMMxx forcefield in GROMACS. I am interested in doing this so myself. Mark Abraham mentioned a Perl script which will do the formatting of the topology file in the required format by GROMACS, so

[gmx-users] make template

Hi, I tried to compile file template.c in the folder share/template and the response is "nothing to be done for all". The suggestion on the mail list copying template.c to subdir tools, doing automake and ./config is not working in my case. When I try to do make -f Makefile.i686-pc-linux-gnu in t

[gmx-users] Question about Athlon 64 4800+ x2 (poor performance)

Dear users I compiled Gromacs-3.3.1 from the src-rpm, on my system x86_64 FC5 (Athlon 64 4800+ x2, 4Gb DDR). When I tested gromacs over one of my molecular system I noticed its very poor performance. Can anybody tell me: 1) What are the defaults setting used by rpmbuild to compile gromacs in

[gmx-users] Accelrys to Gromacs

Dear users, Does anyone know a way to convert a typed structure from Discover Accelrys, using Compass or cvff, and export the structure into a topology and .gro files with all the force field parameters, LJ, bonds, angle, dihedrals ... I have seen this with Lammps (msi2lmp.exe) and I do not know i

Re: [gmx-users] Benchs on gcc and pgi

Hi Erik! Normal simulations aren't using any linear algebra stuff at all. BLAS & LAPACK are only useful when you do matrix stuff, for instance normal mode analysis. Ouch, obvious mistake. Sorry, apologize the error from someone programming too much analysis tolls, rather than the simulation

[gmx-users] Re: TI and heavy H

Thanks David, giving me some hints about what questions I might want to find answers for definetely sets me on the right track! Cheers Luther >> I agree that there will be a d(Ekin)/dlambda term. It will actually >> occur >> independent of whether I shift mass from the oxygen to the dummy atom

Re: [gmx-users] errors on restart

On Thursday 18 May 2006 18:42, Mark Abraham wrote: > gianluca santarossa wrote: > > I think you are right. I guess this is the best solution, after all. > > The drawback is that I need to do a pilot run for each system I need to > > simulate. And the number of processors I choose, too. O, no! It sm

Re: [gmx-users] microcanonical

karamyog singh wrote: Well, I am back. Remember my first and second mdruns. In my second, after stablizing my initial configuration in the 1st md run, I used cut off upto 6.3 whereas the potential minima is at 0.309. 6.3 is quite large a distance compared to 0.309. In the second run, the kinet

Re: [gmx-users] errors on restart

gianluca santarossa wrote: I think you are right. I guess this is the best solution, after all. The drawback is that I need to do a pilot run for each system I need to simulate. And the number of processors I choose, too. O, no! It smells like a benchmark :P Well in the real world, your

Re: [gmx-users] microcanonical

Well, I am back. Remember my first and second mdruns. In my second, after stablizing my initial configuration in the 1st md run, I used cut off upto 6.3 whereas the potential minima is at 0.309. 6.3 is quite large a distance compared to 0.309.  In the second run, the kinetic energy increases which

[gmx-users] No default bond,angle,dihedral types

Dear All, I am planning to simulate a dendrimer molecule using Gromacs.I have successfully used pdb2gmx in order to obtain .top and .gro files but when i used grompp i got lots of warning messages like these below: No default bond types,using zeroes. No default angle types,using zeroes. No default

Re: [gmx-users] errors on restart

Mark Abraham wrote: I can't. I run simulations on a cluster through a queue, and sometimes the jobs are longer than the max time of the queue. Yes you can. Do a pilot run and look at the last few lines of the logfile - or better one of the crashed runs - you want reasonable length so your set

[gmx-users] Re: graph edges problem

oops, i just saw berk hess's message that using pbc=full will circumvent this problem. however, pbc=full is incompatible with shake, right? and my solvent has coupled angle constraints which stuff up lincs. any other way around the problem? cheers mo __

Re: [gmx-users] errors on restart with tpbconv

gianluca santarossa wrote: Florian Haberl wrote: Hi, if the run died before wrting out a complete frame you have to restart from the last complete frame. I agree :), but is there a way to check out automatically the last useful frame? If, as I think, ener.edr is written after (or less f

Re: [gmx-users] errors on restart with tpbconv

Florian Haberl wrote: Hi, if the run died before wrting out a complete frame you have to restart from the last complete frame. I agree :), but is there a way to check out automatically the last useful frame? If, as I think, ener.edr is written after (or less frequently than) traj.trr, than

Re: [gmx-users] errors on restart

gianluca santarossa wrote: Mark Abraham wrote: You can a) prevent your simulations from crashing, I can't. I run simulations on a cluster through a queue, and sometimes the jobs are longer than the max time of the queue. Yes you can. Do a pilot run and look at the last few lines of the lo

Re: [gmx-users] errors on restart

Mark Abraham wrote: You can a) prevent your simulations from crashing, I can't. I run simulations on a cluster through a queue, and sometimes the jobs are longer than the max time of the queue. b) restart from the last frame common to both files, here 8, or Ok, I want to do it automatically...

Re: [gmx-users] errors on restart with tpbconv

Hi, if the run died before wrting out a complete frame you have to restart from the last complete frame. tpbconv -time real -1 Continue from frame at this time (ps) instead of the last frame greetings, florian On Thursday 18 May 2006 14:12, gianluca san

Re: [gmx-users] errors on restart

gianluca santarossa wrote: Dear gmx users, sometimes my simulations crash, and I need to restart them using the command $ tpbconv -f traj.trr -e ener.edr This shouldn't work, you need to give it a .tpr file too. Sometimes it runs, while sometimes it gives me an error. This is part of the ou

Re: [gmx-users] errors on restart

Hi Gianluca,the same thing happens to me sometimes too, it seems as if the edr file update is somehow delayed in relation to the other output files, though written with the user defined periodicity. I usually restart from the previous frame. Sorry I can't help more! Greetings,Maria GiovannaOn 5/18/

Re: [gmx-users] errors on restart with tpbconv

gianluca santarossa wrote: Dear gmx users, sorry for repeating the message... Gianluca ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the

[gmx-users] errors on restart with tpbconv

Dear gmx users, I sometimes need to recover a simulation after a crash, using the command tpbconv -e -f It usually works, but sometimes it exists with errors like: READING COORDS, VELS AND BOX FROM TRAJECTORY traj.trr... trn version: GMX_trn_file (single precision) Read frame 11: step 5000

[gmx-users] errors on restart

Dear gmx users, sometimes my simulations crash, and I need to restart them using the command $ tpbconv -f traj.trr -e ener.edr Sometimes it runs, while sometimes it gives me an error. This is part of the output of tpbconv: trn version: GMX_trn_file (single precision) Read frame 11: step 500

[gmx-users] (no subject)

*Gtk-CRITICAL **: gtk_file_system_path_is_local: assertion `path != NULL' failed*** what is meant by this message? -karamyog. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-

Re: [gmx-users] microcanonical

karamyog singh wrote: I know where the minimum is and I said exactly what you did. However I interpreted the potential becoming 0 as the point before r-min. The potential once becomes 0 before minimum potential value. I thought you were referring to that point and that is why i got confused and

Re: [gmx-users] microcanonical

I know where the minimum is and I said exactly what you did. However I interpreted the potential becoming 0 as the point before r-min. The potential once becomes 0 before minimum potential value. I thought you were referring to that point and that is why i got confused and asked you further questio

Re: [gmx-users] microcanonical

karamyog singh wrote: I placed the atoms randomly means i used random atomic positions, not velocities. The velocities were 0 initially and then I generated velocities at 0.01 K.(1st MD run to get a stable configuration) After that I subjected this structure that I got to NVE.(2nd MD run) Now o

Re: [gmx-users] Pass 11

Alessandro Mattozzi wrote: Hi all Hi, does anybody now how to get a Pass11- like program (freeware, obviously :-))? Any suggestion on free volume assessment by spheres (or generally speaking geometrical body, not necesarily sphere) insertion is welcome! do you mean PASS? It's freeware: htt

Re: [gmx-users] microcanonical

I placed the atoms randomly means i used random atomic positions, not velocities. The velocities were 0 initially and then I generated velocities at 0.01 K.(1st MD run to get a stable configuration) After that I subjected this structure that I got to NVE.(2nd MD run) Now over here I will try with n

[gmx-users] Pass 11

Title: Pass 11 Hi all does anybody now how to get a Pass11- like program (freeware, obviously :-))? Any suggestion on free volume assessment by spheres (or generally speaking geometrical body, not necesarily sphere) insertion is welcome! Tkank you Regards Alessandro Mattozzi M.Phil., Ph.D. s

Re: [gmx-users] microcanonical

karamyog singh wrote: I exactly did that. I initially thought that since I have placed the atoms randomly so it is probable that atoms experience large forces and since I am not allowing any temperature scaling etc. , I am getting large KE. Therefore I first minimized my configuration. I got a

Re: [gmx-users] How to selectively making temperature coupling

From: Mark Abraham <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to selectively making temperature coupling Date: Thu, 18 May 2006 18:05:07 +1000 Zhenting Gao wrote: > Hi gmx-users, > > In this paper, > Ota

Re: [gmx-users] How to selectively making temperature coupling

Zhenting Gao wrote: > Hi gmx-users, > > In this paper, > Ota, N. & Agard, D. A. (2005). Intramolecular signaling pathways revealed by > modeling anisotropic thermal diffusion. Journal of Molecular Biology 351, > 345-354. > A good methodology to find the intramolecular allosteric pathway, name

Re: [gmx-users] microcanonical

I exactly did that. I initially thought that since I have placed the atoms randomly so it is probable that atoms experience large forces and since I am not allowing any temperature scaling etc. , I am getting large KE. Therefore I first minimized my configuration. I got a frozen structure by doing

[gmx-users] How to selectively making temperature coupling

Hi gmx-users, In this paper, Ota, N. & Agard, D. A. (2005). Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion. Journal of Molecular Biology 351, 345-354. A good methodology to find the intramolecular allosteric pathway, namely, ATD, is defined. Basicly, A

Re: [gmx-users] New website

Hi Dallas, On May 18, 2006, at 5:00 AM, Dallas B. Warren wrote: Just a FYI for those developing the website, you might want to look into using the OpenSEF component for Joomla. Gets rid of the long, complicated URLs, and means you can specify what the URL should actually look like, no matt

RE: [gmx-users] About calculations of viscosity

From: "Zhao Lifeng" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Subject: [gmx-users] About calculations of viscosity Date: Fri, 12 May 2006 18:47:53 +0800 Dear gmx-users, I¡¯m a new GMX user. I notice from either the user-manual or the references (Palmer, PRE 49 35

Re: [gmx-users] Order parameter

Kushal Seth wrote: Hi All ! Can anyone help me to find the order parameter of cholesterol as a function of distance form the bilayer. I am doing a Lipid bilayer simulation with POPC and Cholesterol. your question is unclear. Thanks a lot in advance. Kushal Seth _