Re: [gmx-users] Parallel Use of gromacs - parallel run is 20 times SLOWER than single node run

Jim Kress wrote: I ran a parallel (mpi) compiled version of gromacs using the following command line: $ mpirun -np 5 mdrun_mpi -s topol.tpr -np 5 -v At the end of the file md0.log I found: M E G A - F L O P S A C C O U N T I N G Parallel run - timing based on wallclock.

[gmx-users] Runtime need of cpp.exe

.. OK. Again, the shipping Win32 version of cpp.exe is perfectly working with Gromacs 64-bit on a opetron m/c which is a x86-64 box. But I guess it (the above cpp.exe) may not work on pure x64 m/c as its not a valid x64 application. Is there a x64 port of cpp.exe is available ? Can we use other

Re: [gmx-users] Runtime need of cpp.exe

Hi Utkal, Cpp.exe is called by grompp to preprocess the topology. Tsjerk On 7/18/07, Utkal Ranjan Pradhan [EMAIL PROTECTED] wrote: Thank you for your reply. But still confused WHY CPP.EXE IS REQUIRED AT RUNTIME ? (Note that, I can build gromacs without cpp.exe with MS VS 2005, but

Re: [gmx-users] Runtime need of cpp.exe

If cpp is not runnable, I would wonder what those GCC guys are working and how you have compiled GROMACS? On 7/18/2007 4:23 PM, Utkal Ranjan Pradhan wrote: …. OK. Again, the shipping Win32 version of cpp.exe is perfectly working with Gromacs 64-bit on a opetron m/c which is a x86-64 box. But

Re: [gmx-users] Runtime need of cpp.exe

Hi, Can we use other (native windows) c preprocessor ? As it says explicitly in the manual, you can use any preprocessor you want. The default force fields have #include and #define statements meant for a C preprocessor, but it's just a matter of pushing the input files through the

Re: [gmx-users] Magic number error

Hi, Great that you solved it. For the record, this is an excellent example why you should never, ever, use soft NFS mounts. If you stick to hard mounts the clients might hang while the server isn't responding, but at least you won't lose data. Cheers, Erik On Jul 18, 2007, at 2:48

Re: [gmx-users] Implicit solvent simulation

Thank you for your kind reply, Stephane. Anyhow it is a little disappointing that Generalized-Born is not implemented in Gromacs. Sincerely, Seungpyo Hong On 7/16/07, Stéphane Téletchéa [EMAIL PROTECTED] wrote: SeungPyo Hong a écrit : Dear gmx-users, Recently I want to perform MD for

Re: [gmx-users] Implicit solvent simulation

SeungPyo Hong wrote: Thank you for your kind reply, Stephane. Anyhow it is a little disappointing that Generalized-Born is not implemented in Gromacs. I've put it on the development TODO list (feel free to volunteer) http://wiki.gromacs.org/index.php/Implicit_Solvent The reason it is not

Re: [gmx-users] Implicit solvent simulation

Hi, Just to let people know in case they are unaware there is a paper where implicit solvent models have been implemented in GROMACS, the paper can be found using the following link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmedpubmedid=15814616 Tom --On Wednesday, July

[gmx-users] mdp file help

I am trying to simulate a single wall CNT in a box filled with water for about 500 ps and 300K just to start and I am having trouble with the mdp file, basicly what should and should not be in it. I just want it generic to start and tune it up later. Here is what I have done so far along with

Re: [gmx-users] Implicit solvent simulation

Dear Tom, The paper is available and was mentioned in the list. The model, however, isn't available AFAIK. Ran. TJ Piggot wrote: Hi, Just to let people know in case they are unaware there is a paper where implicit solvent models have been implemented in GROMACS, the paper can be found

Re: [gmx-users] Implicit solvent simulation

If you REALLY want implicit solvent then i suggest you contact the authors and ask them about it, however i (like most others i think) have never needed to use implicit solvent. Tom --On Wednesday, July 18, 2007 16:17:01 +0200 Ran Friedman [EMAIL PROTECTED] wrote: Dear Tom, The paper is

[gmx-users] ACE group parameter error un ffG53a5-6?

Dear all Sorry for repeating this message. I have found what appears to be an error in the files ffG53a(5 and 6).rtp related to the ACE group topology. Maybe it is a trivial error, or a change due to something I am missing. I’m sure you experts will ponder it much better than me. I was

RE: [gmx-users] Implicit solvent simulation

I asked for and received the code a couple of years ago. As the paper indicates, it's in an ancient version of GROMACS...which creates challenges. Also, the different models (Still, etc.) are implemented in independent versions of the code. Also, the GB part is actually implemented in FORTRAN.

Re: [gmx-users] mdp file help

You can get a typical mdp file from some tutorials. By the way, I think the topology is wrong. Thanks. On 7/18/07, Christopher Stiles [EMAIL PROTECTED] wrote: I am trying to simulate a single wall CNT in a box filled with water for about 500 ps and 300K just to start and I am having trouble

[gmx-users] genion - hangs up

Dear all, I am having problem with genion. I have already search the gmx archive, and got the following message: While using genion with -np 3, i get 2 lines of Replacing sol. xxx with Na and it hangs up. With -np 1 it works fine and replaces 1 SOL with Na. I thought it might be my system,

Re: [gmx-users] Implicit solvent simulation

Moore, Jonathan (J) a écrit : I asked for and received the code a couple of years ago. As the paper indicates, it's in an ancient version of GROMACS...which creates challenges. Also, the different models (Still, etc.) are implemented in independent versions of the code. Also, the GB part is

Re: [gmx-users] Implicit solvent simulation

Stéphane Téletchéa wrote: Moore, Jonathan (J) a écrit : I asked for and received the code a couple of years ago. As the paper indicates, it's in an ancient version of GROMACS...which creates challenges. Also, the different models (Still, etc.) are implemented in independent versions of the

[gmx-users] Re: Parallel Use of gromacs - parallel run is 20 times SLOWER than single node run (Jim Kress)

It's a 3.712 cube containing 1722 tip4p water molecules at 300 deg K and density = 1000kg/l Regards, Jim Kress ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] Implicit solvent simulation

Hi, On Jul 18, 2007, at 5:08 PM, David van der Spoel wrote: The version used by Alan Mark has never made it into gromacs. Rather, Erik Lindahl started the implementation of this stuff but did never finish it completely, due to other priorities I presume. We should however take out the

Re: [gmx-users] Re: Parallel Use of gromacs - parallel run is 20 times SLOWER than single node run (Jim Kress)

Hi Jim, That system should scale quite well with a fast network (infiniband) since you don't seem to be using PME, and the CVS 3.99 version is even better. However, as David already mentioned, the gigabit network is likely limiting you. If you test the CVS code there are timing reports

[gmx-users] uniform dielectric constant

Reading the mailing list and the wiki as well, I see that GROMACS has little support for implicit solvent. However, I'm interested in simulating charged polymers (small spheres connected with springs) in an aqueos salt solution (more spheres). Assuming no dielectric boundaries -- i.e. a

Re: [gmx-users] uniform dielectric constant

Mikael Lund wrote: Reading the mailing list and the wiki as well, I see that GROMACS has little support for implicit solvent. However, I'm interested in simulating charged polymers (small spheres connected with springs) in an aqueos salt solution (more spheres). Assuming no dielectric

Re: [gmx-users] Implicit solvent simulation

Selon Erik Lindahl [EMAIL PROTECTED]: Hi, On Jul 18, 2007, at 5:08 PM, David van der Spoel wrote: The version used by Alan Mark has never made it into gromacs. Rather, Erik Lindahl started the implementation of this stuff but did never finish it completely, due to other priorities I

Re: [gmx-users] Implicit solvent simulation

[EMAIL PROTECTED] wrote: Selon Erik Lindahl [EMAIL PROTECTED]: Hi, On Jul 18, 2007, at 5:08 PM, David van der Spoel wrote: The version used by Alan Mark has never made it into gromacs. Rather, Erik Lindahl started the implementation of this stuff but did never finish it completely, due to

[gmx-users] install problem

Hi, I am a beginning user of GROMACS, and am just now trying to get a functional installation. There is something not quite right about the installations I have tried. I have spent considerable time testing ideas about what might be the problem, but have not nailed it. I am hoping

Re: [gmx-users] install problem

John Mercer wrote: Hi, I am a beginning user of GROMACS, and am just now trying to get a functional installation. There is something not quite right about the installations I have tried. I have spent considerable time testing ideas about what might be the problem, but have not nailed it.

Re: [gmx-users] How to include Mg in the input file?

srinivas aripirala wrote: Hello everybody, I am attaching both the pdb and the inp. while i was trying to run the inp file. It errors our saying the Mg (magnesium ) ERROR PCM SPHERE(S) MUST HAVE A POSITIVE RADIUS Guys when i diagonize i see that there it has included radius for

[gmx-users] Re: Install problem

-- next part -- A non-text attachment was scrubbed... Name: GME_final.inp Type: application/octet-stream Size: 7224 bytes Desc: not available Url : http://www.gromacs.org/pipermail/gmx-users/attachments/20070718/c0a6ed0c/GME_final.obj -- next part -- A non

Re: [gmx-users] Implicit solvent simulation

There is a niche for implicit solvent if you need to do more extensive conformational sampling than you can achieve with atomically detailed solvent---and if you can plausibly argue that you are not introducing such egregious systematic errors that you are just sampling more junk. At 09:23

Re: [gmx-users] mdp file help

Probably, you've broken your line endings transferring to/from a Windows machine. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search

Re: [gmx-users] mdrun -rerun problems

George Abadir wrote: Hi all, I am running simulations of carbon nanotubes and amino acids in water. I need to calculate the potential energies for the whole system as well as the interaction energy between the CNT and amino acid. What I am tried to do is to calculate the energy for

Re: [gmx-users] mdrun -rerun problems

Yes of course I looked at the output but I thought is I specify energy groups it will output only those specified and not the whole system. However I tried a short run and it did output both. For the crash it turned out it is because all the nodes try to read the huge trajectory file at the

[gmx-users] GAMESS-US for Hybrid QM/MM

Hi All Is there any way to use gamess-us for Hybrid QM/MM calculation with Gromacs instead of using CPMD, GAMESS-uk or gaussion? Thanks Dhiraj winmail.dat___ gmx-users mailing listgmx-users@gromacs.org