[gmx-users] Alternate to xmgrace

Dear Mark, Hi ! Is there any alternate software to xmgrace, which I can use for my MD simulation results and which is compatible with gromacs? As I have installed xmgrace in my computers but the xmgrace window icons and tool bar is not shown properly. Regards, Lal badshah Send instant

[gmx-users] Equilibration

Hi, Can anyone please tell me How to remove the equilibration time from calculating averages. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing list

Re: [gmx-users] Equilibration

Arnab Senapati wrote: Hi, Can anyone please tell me How to remove the equilibration time from calculating averages. Start by looking at the commmand line options for the tools you're using, e.g. -b. Otherwise, your question is too general to get a specific answer. Mark

Re: [gmx-users] Alternate to xmgrace

s lal badshah wrote: Dear Mark, Hi ! Is there any alternate software to xmgrace, which I can use for my MD simulation results and which is compatible with gromacs? As I have installed xmgrace in my computers but the xmgrace window icons and tool bar is not shown properly. Check out

Re: [gmx-users] (no subject)

Hi Arnab, If you know the time at which you want to start the analysis, you can use the -b option (with whatever analysis tool). E.g. starting rmsf calculation at 1 ns: g_rmsf -s topol.tpr -f traj.xtc -o rmsf.xvg -b 1000 Cheers, Tsjerk On 5/5/08, Arnab Senapati [EMAIL PROTECTED] wrote: Hi,

Re: [gmx-users] (no subject)

Hi, On Monday, 5. May 2008 10:53, Arnab Senapati wrote: Hi, Can anyone please tell me How to remove the equilibration time from calculating averages. use -b (begin) -e (end) in the analyse tools to specifiy times. greetings, Florian --

[gmx-users] benchmark: buying a new cluster

Hi all, we are going to buy a new cluster and we are in doubt about the frequency to consider. Basically, we have the possibility to buy either 18 nodes dual quad-core (18x8 cores) bearing Intel-Xeon E5430 2.66 MHz and FSB 1333 MHz or 15 nodes dual quad-core (15x8 cores) bearing Intel-Xeon

[gmx-users] problem with simulation of phosphatidic acid, possibly in my topology?

Hi, I am trying to run a simulation of a POPC bilayer mixed with some mono-anionic Phosphatidic acid (POPA) , where the choline group is replaced by a hydrogen atom. However, the energy of my simulation box diverges, and I am trying to fix the problem. I also tried running a simulation of PA

Re: [gmx-users] benchmark: buying a new cluster

There two CPUs differing not only in frequency but also in FSB speed. But the differences in FSB shall be ignorable for Gromacs. You have two dimensions to think. 1. power of all nodes = number of cores * frequency 2. power of a single node. If you intend to have one simulation running just on

[gmx-users] Parallel processing

Hi all. First, excuse my English, it is not too good, but I'm learning. I have a problem with my gromacs. I have a Dell Precision 470 (2 Xeon processor with 2Gb RAM) and I can't run mdrun_mpi for 2 processor. I describe what is happening. I installed gromacs-3.3.3-1.x86_64.rpm and

[gmx-users] Is such hardware suitable for gromacs

ASUS DSBV-DX/C or Intel S5000VSA E5410 2.33 * 2 FB-DIMM 1G * 8... I could only find some body test their E5410 on Gromacs in google, but I am not sure this suit could compile and run Gromacs, I thirst somebody who is using such hardware tell me whether it is or isn't suitable. ..Or

[gmx-users] benchmark: buying a new cluster

To some extent, it depends on your interconnect and the number of atoms in the simulations that you will be doing. If you are using gigabit ethernet, then you may not scale very well beyond 8 cores on these dual node quad cores and so there is an argument to be made for 10% faster. However, if you

Re: [gmx-users] Parallel processing

[EMAIL PROTECTED] wrote: Hi all. First, excuse my English, it is not too good, but I'm learning. I have a problem with my gromacs. I have a Dell Precision 470 (2 Xeon processor with 2Gb RAM) and I can't run mdrun_mpi for 2 processor. I describe what is happening. I installed

Re: [gmx-users] problem with simulation of phosphatidic acid, possibly in my topology?

himanshu khandelia wrote: Hi, I am trying to run a simulation of a POPC bilayer mixed with some mono-anionic Phosphatidic acid (POPA) , where the choline group is replaced by a hydrogen atom. However, the energy of my simulation box diverges, and I am trying to fix the problem. I also tried

[gmx-users] Angle definition in g_hbond ...

dear gmx-users, I have a very fundamental query. I am trying to obtain the backbone hydrogen bonds formed during a 15ns simulation of a 35 long protein. When I do this by using g_hbond and selecting the Backbone groups, I am getting no hydrogen bonds at all . However, when I plot the hydrogen

[gmx-users] double sids error ? what ?!

Hi all, I got a double sids error when using grompp. What does it mean in the first place ? Apparently, it has to do with Lincs making shake-blocks when using constraint = all-bonds. I am simulating two strands of RNA, defined in the same .top file as I want to add some distance restraint

Re: [gmx-users] Angle definition in g_hbond ...

sharada wrote: dear gmx-users, I have a very fundamental query. I am trying to obtain the backbone hydrogen bonds formed during a 15ns simulation of a 35 long protein. When I do this by using g_hbond and selecting the Backbone groups, I am getting no hydrogen bonds at all . However, when I

Re: [gmx-users] Angle definition in g_hbond ...

Mark Abraham wrote: sharada wrote: dear gmx-users, I have a very fundamental query. I am trying to obtain the backbone hydrogen bonds formed during a 15ns simulation of a 35 long protein. When I do this by using g_hbond and selecting the Backbone groups, I am getting no hydrogen bonds at

Re: [gmx-users] double sids error ? what ?!

BON Michael wrote: Hi all, I got a double sids error when using grompp. What does it mean in the first place ? Apparently, it has to do with Lincs making shake-blocks when using constraint = all-bonds. I am simulating two strands of RNA, defined in the same .top file as I want to add some

[gmx-users] Re: problem with simulation of phosphatidic acid, possibly in my topology?

PS: My previous email was accidentally sent from the gmail account of my colleague, who uses the same workstation. My apologies. This is just a disclaimer on her behalf. On Mon, May 5, 2008 at 11:34 AM, himanshu khandelia [EMAIL PROTECTED] wrote: Hi, I am trying to run a simulation of a

[gmx-users] Re: Free energy - Hydrogen bond solute-solvent - Ethanol as an example.

Hello all I have tried to reproduce the hydration free energy (TI) of the ethanol from Hess and van der Vegt (JPCB, 110, 17616). The value I have obtained is around 20kJ/mol while the reference value is -20.1kJ/mol (if not the sign ...). If someone can help me find the mistake I

Re: [gmx-users] problem with simulation of phosphatidic acid, possibly in my topology?

Dear Mark, Sorry, perhaps I should have clarified more. I did not just make a blind substitution of a choline by a H-atom. First, I did conserve charge. Second, I did introduce reasonable non-bonded and bonded interaction parameters for the new H-atom. The non-bonded interaction parameters were

[gmx-users] LINCS and parallel simulation

Dear gmx-users, I have a problem concerning LINCS crashes after transfering a simulation into parallel mode. Due to inherent errors in GROMAS 3.3.2 positional restraints applied on multiple molecules of the same kind could not be handled in parallel and I did the initial part of the simulation in

[gmx-users] cannot determin precesion of .trn file

Hi all, I have been trying to simulate octa-alanine peptide in a mixed solvents like as mentioned below on Cluster of 128 nodes. 1. water, Trifluoroethanol 2. water, Guanidium ion, Chloride ion simulation was going on properly till 26 ns.I have extended simulation to 50 ns.simulation runs

Re: [gmx-users] Angle definition in g_hbond ...

Hi, Just calculate the no. of atoms according to the choice of options and manually. you will understand why is it giving the error. Secondly check how gromacs calculate the no. of hydrogen bonds. It uses the cut-off 0.35 nm and 30 in version 3.3.1, but in earlier version the angle cut-off was

Re: [gmx-users] cannot determin precesion of .trn file

[EMAIL PROTECTED] wrote: Hi all, I have been trying to simulate octa-alanine peptide in a mixed solvents like as mentioned below on Cluster of 128 nodes. 1. water, Trifluoroethanol 2. water, Guanidium ion, Chloride ion simulation was going on properly till 26 ns.I have extended simulation to 50

Re: [gmx-users] cannot determin precesion of .trn file

Are you running out of disk space? What does gmxcheck tell you about these .trr files? -Justin Quoting [EMAIL PROTECTED]: Hi all, I have been trying to simulate octa-alanine peptide in a mixed solvents like as mentioned below on Cluster of 128 nodes. 1. water, Trifluoroethanol 2. water,

[gmx-users] stochastic dynamics and barostat in Gromacs

Hi all, I want to simulate a polyelectrolyte chain with its counterions in solution  in NPT ensemble. it is well known that for such a system stochastic dynamics is usually used (Langevin thermostat). However what's the best choice for the barostat in Gromacs for such a system (Berendsen or

[gmx-users] topolbuild 1.1.1, minor revisions to an all-atoms model gromacs topology generator

I have submitted a minor revision of topolbuild that I hope is more portable. Version 1.1.1 is now available in the user contributions at the gromacs web site. The following revisions have been made: 1. Removed all non-pointer references to NULL. 2. Gave all external variables single defining

[gmx-users] (no subject)

Hello, I was trying to run a simple LJ system. In the conf.gro box size is 7.52 (cubic). But in the confout.gro the box size is 9.1. Is this possible? -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

[Fwd: [gmx-users] (no subject)]

Hello, I was trying to run a simple LJ system. In the conf.gro box size is 7.52 (cubic). But in the confout.gro the box size is 9.1. Is this possible? -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

[gmx-users] Box size Increase

Hello, I was trying to run a simple LJ system. In the conf.gro box size is 7.52 (cubic). But in the confout.gro the box size is 9.1. Is this possible? -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

Re: [gmx-users] Box size Increase

Arnab Senapati wrote: Hello, I was trying to run a simple LJ system. In the conf.gro box size is 7.52 (cubic). But in the confout.gro the box size is 9.1. Is this possible? Yes, since it happened. :-) If you're trying to understand what it is that you've done that has caused the change,

[gmx-users] (no subject)

Hi, can anyone tell me how to run a NVT simulation in gromacs. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] NVT simulation

- Hi, can anyone tell me how to run a NVT simulation in gromacs. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] (no subject)

Arnab Senapati wrote: Hi, can anyone tell me how to run a NVT simulation in gromacs. Yes. However the existence of this mailing list doesn't absolve you of the need to attempt to find solutions for yourself, do tutorials, do background reading, and experiment for yourself. For your