Re: [gmx-users] Trajectory files are too big

Thank a lot. I am getting the clue for it. Thank all of you. On Jan 23, 2008 4:50 AM, Mark Abraham <[EMAIL PROTECTED]> wrote: > Nabajyoti Goswami wrote: > > Dear Gromacs Users, > > > > After a long time I am working with gromacs. Though at the starting I > > got some problem in installation with

[gmx-users] Re: problems with double precision gmx - solved

Thanks to the reply by David Osguthorpe (which I read only after I sent my last mail) i managed to compile a working double precision gmx. (by simply "make distclean" in the single precision gmx tree before compiling the double precision version) cheers, mic ___

[gmx-users] problems with double precision gmx

Hi everybody, I keep having difficulties when trying to use the double precision version of Gromacs. Typically i get infinte forces at step one of a simulation with double precision while the same system behaves perfectly well with single precision. Below i give an example of what i see when

Re: [gmx-users] Trajectory files are too big

Nabajyoti Goswami wrote: Dear Gromacs Users, After a long time I am working with gromacs. Though at the starting I got some problem in installation with the rpm, (a conflict error with mono-web) I installed it anyway forcefully. Problem is the trajectory files that I am getting are too big. I

Re: [gmx-users] Is there any chance to concatenate (fast) more than 1000 energy files....

Sergio wrote: Hi all I'm trying to concatenate more than 1000 energy files, using a bash script which runs eneconv program. The problem is that it takes a lot of time to do it. Could anyone give me any suggestion of how to improve this task? You only need one invocation of eneconv... see th

Re: [gmx-users] Is there any chance to concatenate (fast) more, than 1000 energy files....

Wouldn't it be a lot easier to just do: eneconv -f *.edr Or am I misunderstanding what you're trying to accomplish? -Justin Quoting Sergio <[EMAIL PROTECTED]>: > Dear Diego I'm not sure whether I am understanding well what you suggest > me. The fact is that I have 1000 energy files to concaten

[gmx-users] Is there any chance to concatenate (fast) more, than 1000 energy files....

Dear Diego I'm not sure whether I am understanding well what you suggest me. The fact is that I have 1000 energy files to concatenate in one PC. My bash script takes the fist two files and concatenates them to produce a temporary output file (using eneconv), after that it concatenates the last

[gmx-users] [gmx-developers] double precision, gmx-3.3.1 and 3.3.2 do not work for me

Hi, Sorry for the delay but Im having problems with sending email to this list - some spam filters must be at work. I think Ive had the same problem - at least the symptoms were the same - a running single precision dataset when supplied to a double precision program gave instant infinite for

Re: [gmx-users] solvent within 3.5 angstrom of protein.

[EMAIL PROTECTED] wrote: Hi, Im attempting to get all solvent within 3.5 angstrom of the protein and not doing well so far. This is for a system using dodecahedral periodic boundary conditions. Ive tried the various -pbc options on trjconv - in particular cluster but I dont think this ha

[gmx-users] solvent within 3.5 angstrom of protein.

Hi, Im attempting to get all solvent within 3.5 angstrom of the protein and not doing well so far. This is for a system using dodecahedral periodic boundary conditions. Ive tried the various -pbc options on trjconv - in particular cluster but I dont think this has worked - there are protein

Re: [gmx-users] Virtual site and constraints

Нилов Дмитрий wrote: Thank you very much, but in what way can I define the carbon like massless when it treated as a virtual site(type 3) in formate molecule? You can define it as zero, but take care to get the right moment of inertia (by defining further virtual sites). Grompp runs with er

[Fwd: Re: [gmx-users] mdrun CVS version crashes instantly when run across nodes in parallel]

Hi Erik, I have made a test with today's CVS version and I also run into the problem you described. It happens as soon as one uses more than one node and at the same time more than one process per node. The problem seems to be in gmx_sumd where in the two-step summation in a call to MPI_Allreduce

Re[2]: [gmx-users] Virtual site and constraints

Thank you very much, but in what way can I define the carbon like massless when it treated as a virtual site(type 3) in formate molecule? Grompp runs with error when carbon has mass: converting bonded parameters... # CONNBONDS: 3 # CONSTR: 3 # VSITE3: 1 Setting particle type to V fo

Re: [gmx-users] Is there any chance to concatenate (fast) more than 1000 energy files....

I think it would take more time to transfer files than doing it on a single machine, but here is what I suggest: Assuming you have a cluster of 5 nodes you may concatenate by parts than put it all together, something like this: transfer .edr files to /tmp/ of each node than eneconv the fragments

[gmx-users] Is there any chance to concatenate (fast) more than 1000 energy files....

Hi all I'm trying to concatenate more than 1000 energy files, using a bash script which runs eneconv program. The problem is that it takes a lot of time to do it. Could anyone give me any suggestion of how to improve this task? Thank you in advance. -- Alberto Sergio Garay Practica Profesi

Re: [gmx-users] FEP trajectory errors

Yep, all atoms begin to freezeeven the ones not being perturbed (i.e. the water molecules). It's pretty strange. It only happens for lambda=1.0. Below is my .mdp file. ; Run Control integrator = md ; calculation type dt = 0.0015

Re: [gmx-users] Cuted trr file not readable

Edvin Erdtman wrote: Hi I have made a mistake... I have deleted the trr file while computing. The system continue saving to the same filename, but the first 950 ps is lost. that is ok I don't need it, but now I want to enlong the simulation by using tpbconv. The file is not readable since it c

[gmx-users] Cuted trr file not readable

Hi I have made a mistake... I have deleted the trr file while computing. The system continue saving to the same filename, but the first 950 ps is lost. that is ok I don't need it, but now I want to enlong the simulation by using tpbconv. The file is not readable since it can not determine the

Re: [gmx-users] mdrun CVS version crashes instantly when run across nodes in parallel

Hi Erik, have you tried the small MPI test program to which your link points? > http://www.open-mpi.org/community/lists/users/2006/04/0978.php This would help to figure out whether the problem is on the Gromacs or on the MPI side. From the result that Gromacs 3.3.x works on your cluster, unfortun

[gmx-users] mdrun CVS version crashes instantly when run across nodes in parallel

Hello Gromacs users. In the CVS version, I experience that mdrun crashes instantly when run in parallel across nodes (for any simulation system). The cluster consists of 8 nodes with Intel 6600 Quad-Core processors. As long as a job is run on a single node (using 1,2 or 4 CPU:s) everything works f

Re: [gmx-users] grompp error with charmm

On 22 Jan 2008 11:10:47 - "sarbani chattopadhyay" <[EMAIL PROTECTED]> wrote: hi, I am trying to run gromacs using charmm but I am facing the following error while running the "grompp" command checking input for internal consistency... calling /usr/local/bin/cpp... topol.top:11:24: /

[gmx-users] grompp error with charmm

 hi, I am trying to run gromacs using charmm but I am facing the following error while running the "grompp" command checking input for internal consistency... calling /usr/local/bin/cpp... topol.top:11:24: /usr/local/gromacs/share/gromacs/top/ffcharmm.itp: Permission denied topol.top:696

Re: [gmx-users] Protein Moving Out of Box in ED

On Tue, 22 Jan 2008 08:39:04 + (GMT) Anirban Ghosh <[EMAIL PROTECTED]> wrote: Hi Friends, I am simulating a 463 aa protein in water only along the 1st Eigen Vector i.e. I am trying to do Essential Dynamics along First Principle Component. I have used the make_edi command to generate a .edi

Re: [gmx-users] Trajectory files are too big

You can reduce the size of the trajectories after the simulation with trjconv -skip (or -dt). For a new simulation I refer to the previous suggestion. Andreas Nabajyoti Goswami wrote: Dear Gromacs Users, After a long time I am working with gromacs. Though at the starting I got some problem i

Re: [gmx-users] FEP trajectory errors

Do really all atoms "freeze". So also the atoms, which are not perturbed? Can you post your mdp-file? Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 231

[gmx-users] Protein Moving Out of Box in ED

Hi Friends, I am simulating a 463 aa protein in water only along the 1st Eigen Vector i.e. I am trying to do Essential Dynamics along First Principle Component. I have used the make_edi command to generate a .edi file and then using it to run the mdrun. But my problem is that every time after a

[gmx-users] R:Re: problem with GROMACS parallelization

Dear Marc, dear Carsten, I was out of office and I read only today your suggestions about GROMACS parallelization. I will try to apply your suggestions. This is only to thank you for your interest. Best regards Anna Marabotti ___ gmx-users mailing list