Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu)

Hi,Thanks. I have test different cpus. Our institute has two clusters: one is each node has 4 cpu (A), one is one node has only 1 cpu (B). I made different tests on the two clusters and my local computer using the same system. See the following result: A (For 1 hour) # of cpus ; MD steps 4

[gmx-users] g_order C code

Dear Gromacs users, Hie, I am calculating the order parameters for a bilayer patch using g_order analysis tool in gromacs version 3.3. I have a total of 48 elements in the patch and I want the order parameter value for each and every element i.e. a total of say 48 values for order parameter

Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu)

On Thursday 14 September 2006 09:53, Mark Abraham wrote: Qiao Baofu wrote: Hi, Thanks. I have test different cpus. Our institute has two clusters: one is each node has 4 cpu (A), one is one node has only 1 cpu (B). I made different tests on the two clusters and my local computer using

[gmx-users] Re: Re: Re: Question about parallazing Gromacs

-- Message: 7 Date: Thu, 14 Sep 2006 09:27:45 +0200 From: Qiao Baofu [EMAIL PROTECTED] Subject: Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED]

Re: [gmx-users] g_order C code

On Thu, 2006-09-14 at 02:21 -0700, priyanka srivastava wrote: Dear Gromacs users, Hie, I am calculating the order parameters for a bilayer patch using g_order analysis tool in gromacs version 3.3. I have a total of 48 elements in the patch and I want the order parameter value for each

Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu)

2006/9/14, Mark Abraham [EMAIL PROTECTED]: Probably your interconnects between nodes are using carrier pigeons orsomething :-) I expect that 1 cpu on machine A will require around fourtimes as long as 1 4-cpu node, which you can presumably test for yourself. It is forbidden to run only one cpu on

Re: [gmx-users] g_order C code

Thank you for your reply. I am also curious to know if this is the right way of doing it. I am not sure of the changes that I have made in the code. Any suggestions on that please? Since, when I say make install it gives the following error: cc -DHAVE_CONFIG_H -I. -I. -I../../src

Fwd: [gmx-users] Hi...

Hi all.. I wrote this mail yesterday. But could not receive any reply till now. So if someone can suggest something about it. That would be nice. Best regardsNavBegin forwarded message:From: Navratna Vajpai [EMAIL PROTECTED]Date: September 13, 2006 10:32:21 AM GMT+02:00To: Discussion list for

[gmx-users] short range nonbondeds = 0 in power4

Hi, I've run into a mysterious problem. The versions 3.3. and 3.3.1 compile and execute, but the short range coulomb and LJ energies come out as zero when using the mpi-version. Serial code works ok (mpi version gives zero if run using just one cpu). No errors, no warnings. I've tried using

Re: [gmx-users] why the backbone can be broken during MD process

Fan, Fenghui wrote: Dear all, Will you please tell me why the backbone can be broken during MD process and how can we fix them? I am looking forward to getting your reply. it can not. please be more specific. Best regards. Fenghui Fan ___

Re: [gmx-users] short range nonbondeds = 0 in power4

Atte Sillanpää wrote: Hi, I've run into a mysterious problem. The versions 3.3. and 3.3.1 compile and execute, but the short range coulomb and LJ energies come out as zero when using the mpi-version. Serial code works ok (mpi version gives zero if run using just one cpu). No errors, no

Re: [gmx-users] Hi...

As suggested by you I tried using the g_angle. But got tucked. It asks for a .ndx file. I tried making it using mk_angndx but gave me an error when i used the option -type phi-psi. Although it worked well when I used the option dihedral instead of phi-psi. The .ndx file has strange nomenclature

Re: [gmx-users] CHARMM force field implementation in Gromacs :

Thanks for your answers (I had forgotten this comment in the script). The problem is that most of dihedral with multiplicity n = 6 don't come alone. For exemple in Arg : HD1 HE || |// --CG--CD--NE--CZ || \ HD2 is defined by 6 dihedral with n=6

Re: Fwd: [gmx-users] Hi...

Dongsheng Zhang wrote: On Thu, 2006-09-14 at 06:36 -0700, David van der Spoel wrote: Navratna Vajpai wrote: Hi all.. I wrote this mail yesterday. But could not receive any reply till now. So if someone can suggest something about it. That would be nice. Best regards Nav Begin forwarded

Re: [gmx-users] short range nonbondeds = 0 in power4

Atte Sillanpää wrote: On Thu, 14 Sep 2006, David van der Spoel wrote: I've run into a mysterious problem. The versions 3.3. and 3.3.1 compile and execute, but the short range coulomb and LJ energies come out as zero when using the mpi-version. Serial code works ok (mpi version gives zero if

[gmx-users] Question about use of tpbconv

Hi I have a quick question. When you use tpbconv to continue runs what exactly is taken from the *.edr and *.trr files? For instance if I have to run my simulation in short batches of 1ns is it sufficient to just use the run3 files to continue the run (2ns-3ns) or should thr run1, run2 and

[gmx-users] CHARMM force field : TIP3 LJ parameters

Hello everybody, sorry to bother you with my problems another time. I have checked the non-bonded parameters from Yuguang Mu's ffcharmmnb.itp. The parameters for TIP3 atoms (CHARMM's water model) are : c6c12 HT 1.008 0.000 A

Re: [gmx-users] CHARMM force field implementation in Gromacs :

Nicolas SAPAY wrote: Thanks for your answers (I had forgotten this comment in the script). The problem is that most of dihedral with multiplicity n = 6 don't come alone. For exemple in Arg : HD1 HE || |// --CG--CD--NE--CZ || \ HD2 is defined by

[gmx-users] Why RMSFs of some protein chains in my system are unreasonably large?

Dear all, I finish a 10-ns MD simulations for a system including 16 lysozyme molecule chains, some solvents H2O molecules and 128 Cl- counter ions under PBC. When I use the command to calculate the RMSF of residues as follows: g_rmsf -f ***.xtc -s ***.tpr -o rmsf_res.xvg (I selected 3

RE: [gmx-users] Surface Tension Calculation

I posted a question a few days ago regarding the calculation of the surface tension of a lipid bilayer in Gromacs. The response that I got was to use the option #Surf*SurfTens in g_energy. I am not really sure how to do this. I have looked at the g-energy file in Gromacs, and I

Re: [gmx-users] periodic boundary condition

Cherry Y. Yates wrote: Dear gromacs developers and users, I am calculating a nanotube which has periodic boundary condition along one direction. I wonder how to make an itp file for this system. The difficulty lies in describing the bond between two end atoms, e.g., two atoms are bonded in

Re: [gmx-users] Surface Tension Calculation

toma0052 wrote: Hi, I posted a question a few days ago regarding the calculation of the surface tension of a lipid bilayer in Gromacs. The response that I got was to use the option #Surf*SurfTens in g_energy. I am not really sure how to do this. I have looked at the g-energy file in

[gmx-users] mdp wrong

hi followthe lastproblem ,i checked my gro,itp and modifid,but this time ,"invalid command line argument",what's that mean? is still my mdp'wrong?but this mdp that i test well in other gro ,and itp in ffgrom96,and this time ,my forcefield is ffoplsaa,is there any different in the mdp? 3G 时 代 来

[gmx-users] Re: gmx-users Digest, Vol 29, Issue 49

Hi Joanna, You can use your last *.tpr/trr/edr files to continue a simulation. The only thing to be aware is if the integrity of the last files is conserved. If not (for example after a system crash), you should exclude the last frame in order to avoid inconsistencies. Regards, César.-