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

2006-09-14 Thread 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 s

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

2006-09-14 Thread Mark Abraham
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 the same system. See the following result: A (For 1 hou

[gmx-users] g_order C code

2006-09-14 Thread priyanka srivastava
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 along

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

2006-09-14 Thread Florian Haberl
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 comp

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

2006-09-14 Thread Cesar Araujo
-- 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" Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain;

Re: [gmx-users] g_order C code

2006-09-14 Thread Erik Marklund
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 fo

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

2006-09-14 Thread Qiao Baofu
Thanks a lot!2006/9/14, Cesar Araujo <[EMAIL PROTECTED]>: > -->> 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 us

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

2006-09-14 Thread 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 o

Re: [gmx-users] g_order C code

2006-09-14 Thread priyanka srivastava
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 -I/usr/X11R

Re: [gmx-users] g_order C code

2006-09-14 Thread Erik Marklund
I have never done any lipid order stuff and I don't know that much about the underlying theory, so the only help I can offer concerns progamming only. It seems I have a different version of gmx_order.c, where the problematic parts of the code are around lines 448 and 497. I think, however, that I

Re: [gmx-users] g_order C code

2006-09-14 Thread priyanka srivastava
thanks again for your prompt reply. Okey, and I am not good at programming at all :-) By looking at the gmx_order.c program could u tell me which flag is i.e. index[i] or only [i] is indicating the elements of a group? Supppose there are 14 groups (i guess denoted by ngrps in the code) and each

Fwd: [gmx-users] Hi...

2006-09-14 Thread Navratna Vajpai
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 GRO

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

2006-09-14 Thread David van der Spoel
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 message: *From: *Navratna Vajpai <[EMAIL PROTECTED] > *Date: *

Re: [gmx-users] g_order C code

2006-09-14 Thread Erik Marklund
Hi again. I've taken a quick glace at the code, trying to figure out what the different structures and variables are all about. Here goes... order seem to be an array of pointers to 3D-vectors (type rvec, that is). ngrps is in this case actually the number of atoms in a group. Therefore (*order)[

Re: [gmx-users] Hi...

2006-09-14 Thread Navratna Vajpai
Sorry for not so explicitly explaining the things.. Here it goesI have a nona peptide and I ran a MD of 20ns using OPLS-AA force field. when I used the OPLS-AA the phi angles came out to be -ve for three of the amino acids. which is stericaly not allowed. But when I ran it using GROMOS I found all

RE: [gmx-users] Hi...

2006-09-14 Thread Mu Yuguang (Dr)
OPLS-aa force field is good for beta structure, it is not so good for alpha helix study. Amber99f force field is good for alpha helix , but not good for beta structure   Best regards Yuguang   Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological

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

2006-09-14 Thread Fan, Fenghui
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. Best regards. Fenghui Fan ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.

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

2006-09-14 Thread Atte Sillanpää
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

2006-09-14 Thread David van der Spoel
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 ___ gmx-u

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

2006-09-14 Thread David van der Spoel
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 warnin

Re: [gmx-users] Hi...

2006-09-14 Thread David van der Spoel
Mu Yuguang (Dr) wrote: OPLS-aa force field is good for beta structure, it is not so good for alpha helix study. Amber99f force field is good for alpha helix , but not good for beta structure Very encouraging... -- David. ___

Re: [gmx-users] Hi...

2006-09-14 Thread David van der Spoel
Navratna Vajpai wrote: Sorry for not so explicitly explaining the things.. Here it goes I have a nona peptide and I ran a MD of 20ns using OPLS-AA force field. when I used the OPLS-AA the phi angles came out to be -ve for three of the amino acids. which is stericaly not allowed. But when I ran

Re: [gmx-users] Hi...

2006-09-14 Thread Navratna Vajpai
You are right .. I have used g_rama for the phi-psi values. I will try g_angle as well. With -ve i meant negative values for the phi angle. As far as I understand negative phi values are sterically  not allowed. let me check with the g_angle as well. Thanks for the answer as well the reference. bes

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

2006-09-14 Thread Mark Abraham
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? It can only be broken if you haven't defined it to be whole, or have done something mind-numbingly hideous elsewhere :-) Check your .top file Mark ___

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

2006-09-14 Thread Dongsheng Zhang
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 m

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

2006-09-14 Thread Atte Sillanpää
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 run using just one cpu).

Re: [gmx-users] Hi...

2006-09-14 Thread Navratna Vajpai
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 whi

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

2006-09-14 Thread Nicolas SAPAY
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 (C

[gmx-users] DPPC Bilayer Size

2006-09-14 Thread Akshay Patny
Hi All   I am trying to simulate a GPCR protein belonging to the rhodopsin family with amino acid length of 320 residues. Also, I would be using the pre-hydrated DPPC bilayer, can somebody suggest that for a GPCR protein of roughly 320 aa, how big DPPC bilayer would be appropriate to use

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

2006-09-14 Thread David van der Spoel
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

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

2006-09-14 Thread David van der Spoel
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 mess

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

2006-09-14 Thread David van der Spoel
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 r

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

2006-09-14 Thread Dongsheng Zhang
On Thu, 2006-09-14 at 13:10 -0700, David van der Spoel wrote: > 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

[gmx-users] Question about use of tpbconv

2006-09-14 Thread Joanne Hanna
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 run3

Re: [gmx-users] Question about use of tpbconv

2006-09-14 Thread Mark Abraham
Joanne Hanna wrote: 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 t

[gmx-users] Surface Tension Calculation

2006-09-14 Thread toma0052
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 Gromacs, and I don't

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

2006-09-14 Thread Atte Sillanpää
On Thu, 14 Sep 2006, David van der Spoel wrote: 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.

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

2006-09-14 Thread Nicolas SAPAY
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 3.1539699357e-

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

2006-09-14 Thread Mark Abraham
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] periodic boundary condition

2006-09-14 Thread Cherry Y. Yates
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 an infinite length system, but a

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

2006-09-14 Thread Hu Zhongqiao
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 f

RE: [gmx-users] Surface Tension Calculation

2006-09-14 Thread Dallas B. Warren
> 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, an

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

2006-09-14 Thread David van der Spoel
Hu Zhongqiao wrote: 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.xv

Re: [gmx-users] periodic boundary condition

2006-09-14 Thread David van der Spoel
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 an

Re: [gmx-users] Surface Tension Calculation

2006-09-14 Thread David van der Spoel
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 Gro

[gmx-users] is it my mdp's wrong?

2006-09-14 Thread zzhwise1
hi all     my system is lb film of 36 c14cooh long chains! my gro and itp wrote correctly,but when i used the l-bfgs to minimize the system ,the grompp show invalid order "moleculetype",when use the MD ,it showed the atom number in gro not the same as in itp?    is it my mdp's wrong?   3G 时 代 来 临

Re: [gmx-users] is it my mdp's wrong?

2006-09-14 Thread David van der Spoel
zzhwise1 wrote: hi all my system is lb film of 36 c14cooh long chains! my gro and itp wrote correctly,but when i used the l-bfgs to minimize the system ,the grompp show invalid order "moleculetype",when use the MD ,it showed the atom number in gro not the same as in itp? is it my mdp's

[gmx-users] mdp wrong

2006-09-14 Thread zzhwise1
  hi   follow the last problem ,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

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

2006-09-14 Thread Cesar Araujo
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.-

RE: [gmx-users] mdp wrong

2006-09-14 Thread Dallas B. Warren
> follow the last problem ,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?