[gmx-users] Re: Unable to install Mac OS X package

Phil Wenzel wrote: Hello again, I have failed about five times in my attempts to install gromacs. I did the following: http://www.gromacs.org/content/view/32/57/ I clicked on: Mac OS X 10.4 * gromacs-3.3.2.pkg.tgz The gromacs-3.3.2.pkg.tgz converted to gromacs-3.3.2.pkg on my mac.

Re: [gmx-users] compilation fails on MAC OSX - Leopard

Hi, Thanks for your reply. I have succeeded to compile Gromacs on Leopard after the two following changes: 1. disabling the optimization for ia32 with the options : --disable- ia32-sse --disable-ia32-3dnow 2. installing open-mpi. For some reason "make" had a problem with the lam-mpi librarie

Re: [gmx-users] compilation fails on MAC OSX - Leopard

Hadas Leonov wrote: Hi, Thanks for your reply. I have succeeded to compile Gromacs on Leopard after the two following changes: 1. disabling the optimization for ia32 with the options : --disable-ia32-sse --disable-ia32-3dnow 2. installing open-mpi. For some reason "make" had a problem with the

[gmx-users] Differences in the bonded potentials in 3.3.2 vs. 3.3.1

I used the same trp file for both runs, which was created with 3.3.1. I also tried by creating the trp with the respective grompp version and the same output resulted. There were no errors or warnings when I ran grompp to create the trp file. Amadeu >* *>* My student and I have been tryi

Re: [gmx-users] Differences in the bonded potentials in 3.3.2 vs. 3.3.1

Amadeu wrote: I used the same trp file for both runs, which was created with 3.3.1. I also tried by creating the trp with the respective grompp version and the same output resulted. There were no errors or warnings when I ran grompp to create the trp file. OK, in that case please submit a

[gmx-users] (no subject)

I am simulating a carbon nanotube in water, I have been able to get it working for the Gromacs force field by modifying ffgmxbon.itp in the following way: # [ bondtypes ] ; i j func b0 kb C C 1 0.14210 478900. # [ angletype

[gmx-users] CNT Simulation with GROMOS96 43a1 force field

I am simulating a carbon nanotube in water, I have been able to get it working for the Gromacs force field by modifying ffgmxbon.itp in the following way: # [ bondtypes ] ; i j func b0 kb C C 1 0.14210 478900. # [ angletype

Re: [gmx-users] CNT Simulation with GROMOS96 43a1 force field

Christopher Stiles wrote: I am simulating a carbon nanotube in water, I have been able to get it working for the Gromacs force field by modifying ffgmxbon.itp in the following way: # [ bondtypes ] ; i j func b0 kb C C 1 0.14210 478900. ###

[gmx-users] How to add calcium ions at desired position?

Hi all, I would like to simulate a protein with calcium ions at the calcium binding sties. I cannot use genion to add calcium ions because genion put the ions randomly. Is there any conventional way to do this? The only way I could think of is the following: 1. Add the calcium ions in the protei

Re: [gmx-users] How to add calcium ions at desired position?

Quoting Peggy Yao <[EMAIL PROTECTED]>: > Hi all, > > I would like to simulate a protein with calcium ions at the calcium > binding sties. I cannot use genion to add calcium ions because genion > put the ions randomly. Is there any conventional way to do this? > > The only way I could think of is t

Re: [gmx-users] How to add calcium ions at desired position?

step 4) shall be add water, minimize energy. step 5) it's a bad idea to couple ion alone, see wiki pls. step 6,7) you shall at least have two stages, em, eq before production md. On 11/19/2007 5:23 AM, Peggy Yao wrote: Hi all, I would like to simulate a protein with calcium ions at the calcium

[gmx-users] Extending MD run

Hi all, In gromacs if you want to extend your run you can do something like > grompp_d -f md.mdp -c MD1.gro -p mol.top -t rom_MD1.trr -e from_MD1.edr -o for_MD2.tpr Now my question is, what happen if the trr file ends at 400ps and the edr file ends at 399ps? Will it use the trr alone and for

[gmx-users] floating point exception for grompp -e ener.edr on some clusters

Very dificult to debug without access to the machine. It could be due to a weird bug that only shows up with certain compilers or it could be a compiler problem. We have most experience with gcc, and its quirks. Most of the gcc related problems have been worked around. If you can try with a

Re: [gmx-users] Extending MD run

Check out: http://wiki.gromacs.org/index.php/Doing_Restarts I think the tpbconv tool might be of more use in your case. Choose a frame that is present in both your .edr and .trr, and specify this time as your restart point with the -time option. -Justin Quoting Itamar Kass <[EMAIL PROTECTED]>:

Re: [gmx-users] Extending MD run

Thank Justin, Still I am wondering about the grompp option, 'cause this is what I use most. You my also say I am invested in this (in CPU time manner). Itamar Justin A. Lemkul wrote: Check out: http://wiki.gromacs.org/index.php/Doing_Restarts I think the tpbconv tool might be of more use i

Re: [gmx-users] Extending MD run

Hi Itamar, I suppose you could try setting tinit within the .mdp file to a frame that is present in both the .edr and .trr (similar to the -time suggestion for tpbconv), and start from that point. I do believe both the .edr and .trr are required for an exact restart (at least, if you're using pre

Re: [gmx-users] Extending MD run

Itamar Kass wrote: Thank Justin, Still I am wondering about the grompp option, 'cause this is what I use most. You my also say I am invested in this (in CPU time manner). You being cryptic doesn't serve your purpose of getting useful free help :-) Justin's advice was correct but incomplete

Re: [gmx-users] Extending MD run

Quoting Mark Abraham <[EMAIL PROTECTED]>: > Itamar Kass wrote: > > Thank Justin, > > > > Still I am wondering about the grompp option, 'cause this is what I use > > most. You my also say I am invested in this (in CPU time manner). > > You being cryptic doesn't serve your purpose of getting useful

Re: [gmx-users] How to add calcium ions at desired position?

Peggy Yao wrote: Hi all, I would like to simulate a protein with calcium ions at the calcium binding sties. I cannot use genion to add calcium ions because genion put the ions randomly. Is there any conventional way to do this? If you read the man page for genion, you can get some ions generat

Re: [gmx-users] Extending MD run

Justin A. Lemkul wrote: Quoting Mark Abraham <[EMAIL PROTECTED]>: Itamar Kass wrote: Thank Justin, Still I am wondering about the grompp option, 'cause this is what I use most. You my also say I am invested in this (in CPU time manner). You being cryptic doesn't serve your purpose of getting

Re: [gmx-users] Extending MD run

Quoting Mark Abraham <[EMAIL PROTECTED]>: > Justin A. Lemkul wrote: > > Quoting Mark Abraham <[EMAIL PROTECTED]>: > > > >> Itamar Kass wrote: > >>> Thank Justin, > >>> > >>> Still I am wondering about the grompp option, 'cause this is what I use > >>> most. You my also say I am invested in this (i

Re: [gmx-users] Extending MD run

Justin A. Lemkul wrote: If you do this, please report what you see and I'll update the wiki page. From a quick test case, it appears that -time does not override what is specified in the .mdp file. For example, if tinit = 1000 in the .mdp file, but then I issue: $ grompp -f test.mdp -c con

Re: [gmx-users] How to add calcium ions at desired position?

> Never couple solvent and ions separately. Check out: > http://wiki.gromacs.org/index.php/Thermostats > Try tc-grps = Protein Non-protein excuse me, if the system includes lipid bilayer, how should i set the tc-prgs? Protein + Lipids + Sol and Ion? or Protein + Non-protein ? thanks___

Re: [gmx-users] floating point exception for grompp -e ener.edr on some clusters

[EMAIL PROTECTED] wrote: Very dificult to debug without access to the machine. It could be due to a weird bug that only shows up with certain compilers or it could be a compiler problem. We have most experience with gcc, and its quirks. Most of the gcc related problems have been worked around.

[gmx-users] Quasiharmonic entropies

Dear GMX users, This is just a note to let you know that I uploaded a script to calculate the QH entropies from the output of g_covar (or from NMA) to the user contributions section. It should work on GMX 3.2.1 and above. This can be useful until the new g_anaeig is released. Ran.