Re: [gmx-users] old patch for slow networks

Jones de Andrade wrote: Hi all. I'm writing this message to ask a simple and direct question: the available patch of gmx3 for slow networks, that includes the ordered-all-to-all procedures, seems fo be indicated for version 3.1. Hi Jones, this is actually a patch for gromacs 3.3.1. It's st

Re: [gmx-users] Blue Gene/P

Peter Tieleman wrote: Thanks. I've seen the BG/L argument, but BG/P processors are faster. I have no idea how much though, and am looking for actual numbers or if those are not available a guess based on actual BG/L numbers and some argument about scaling to a BG/P. Well I have a BG/L I can r

Re: [gmx-users] Blue Gene/P

Thanks. I've seen the BG/L argument, but BG/P processors are faster. I have no idea how much though, and am looking for actual numbers or if those are not available a guess based on actual BG/L numbers and some argument about scaling to a BG/P. Cheers, Peter Mark Abraham wrote: Peter Tielema

Re: [gmx-users] Blue Gene/P

Peter Tieleman wrote: Hi, Has anyone run benchmarks on a BlueGene/P ? The word from IBM in December was that since GROMACS 3.x would lack both assembly inner-loops and threading on BlueGene/L, that it wasn't worthwhile running GROMACS on onw. I figure that goes for BlueGene/P too. Mark ___

[gmx-users] Blue Gene/P

Hi, Has anyone run benchmarks on a BlueGene/P ? Thanks, Peter ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't

[gmx-users] old patch for slow networks

Hi all. I'm writing this message to ask a simple and direct question: the available patch of gmx3 for slow networks, that includes the ordered-all-to-all procedures, seems fo be indicated for version 3.1. It's still "necessary" for slow networks using gmx3.3? Thanks a lot in advance... Sinceral

Re: Re: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS

Justin, thank you very much for your attention. This is totally my fault. After putting N to the first residue, the column that indicates the coordinates has been flipped to the right. So, the first numbers could not be read by pdb2gmx. That is the source of the problem. However, thank you again

Re: [gmx-users] Converting Tripos FF to Gromacs?

--- serdar durdagi <[EMAIL PROTECTED]> wrote: > Dear all, > > I have made MD simulations of fullerene > derivatives using Tripos FF, for short simulation > time. I would like to extend these simulations using > faster program GROMACS. > > Is there any way to convert Tripos FF and > st

Re: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS

Quoting OZGE ENGIN <[EMAIL PROTECTED]>: > Ok, it should be better to describe the problem in a more detailed way. > I got this structure from Swiss-modeler program. I do not think I have a > problem with the starting structure because I truncated the protein at some > PRO residue, and got no error

Re: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS

Ok, it should be better to describe the problem in a more detailed way. I got this structure from Swiss-modeler program. I do not think I have a problem with the starting structure because I truncated the protein at some PRO residue, and got no error at all. So, there is something wrong about th

[gmx-users] Re: g_sas and vdwradii.dat

Please disregard; I made a typo when selecting my index groups. Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>: > > Hi all, > > I recently completed several simulations of pure DPPC bilayers (128 lipids, > 64 > per leaflet, from Tieleman's site), and am processing the output. Of > interest > to

Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS

Quoting OZGE ENGIN <[EMAIL PROTECTED]>: > I already indicated the problem that I have. If I put an N prefix to the > first residue, I get warning of having "long bonds." It has been indicated in > the mail.Moreover, these long bonds can not be minimized during the > minimization step. Although I p

Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS

I already indicated the problem that I have. If I put an N prefix to the first residue, I get warning of having "long bonds." It has been indicated in the mail.Moreover, these long bonds can not be minimized during the minimization step. Although I put a relatively higher tolerance for the force

Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS

Quoting OZGE ENGIN <[EMAIL PROTECTED]>: > Hi all, > > I am trying to use AMBER ff in GROMACS. I have followed the steps that are > given in the http://chemistry.csulb.edu/ffamber/ link. > > The first residue of the protein is GLN. I put an N prefix to this residue. > The pdg2gmx works well excep

[gmx-users] g_sas and vdwradii.dat

Hi all, I recently completed several simulations of pure DPPC bilayers (128 lipids, 64 per leaflet, from Tieleman's site), and am processing the output. Of interest to me is the SASA, so I'm using g_sas. I ran the command: g_sas -f md_0_100.xtc -s md.tpr -n sas.ndx (selecting solvent for the

[gmx-users] error with pdb2gmx when using AMBER ff in GROMACS

Hi all, I am trying to use AMBER ff in GROMACS. I have followed the steps that are given in the http://chemistry.csulb.edu/ffamber/ link. The first residue of the protein is GLN. I put an N prefix to this residue. The pdg2gmx works well except giving an warning of long bond between some ato

Re: [gmx-users] anisotropic coupling tau_p values

Quoting pragya chohan <[EMAIL PROTECTED]>: > > hi > please refer to my mail > http://www.gromacs.org/pipermail/gmx-users/2008-March/033024.html I posted a > question regarding taup_p to be used with anisotropic coupling. > As qoted "A reasonable choice for relaxation time would be 100 fs. The > co

[gmx-users] anisotropic coupling tau_p values

hi please refer to my mail http://www.gromacs.org/pipermail/gmx-users/2008-March/033024.html I posted a question regarding taup_p to be used with anisotropic coupling. As qoted "A reasonable choice for relaxation time would be 100 fs. The compressibility and the relaxation time appear only as

[gmx-users] Re: Help needed on using general amber force field (GAFF)

There is not really a difference between proper and improper dihedrals in amber the amberFF, the only difference is that improper dihedrals are not serially linked (amber 8 manual page 261). I do not really understand your problem. Are you writing a new topology for a small molecule in the amber

Re: [gmx-users] Re: Help needed on using general amber force field (GAFF) in Gromacs

Hi Servaas, Thanks for your reply. Your inforamtion is very helpful. Now I am trying to write the topology file by myself when dealing with a small molecule. I have know their conversion relationship, but in my case, I want to fix a few atoms in a plane. From the gaff.dat file , I can see the pa

[gmx-users] How to modify H atom type from opls_369 to match H expected by popc.itp

There is no need to post twice, I saw your first post. Your level of questions indicates that you still do not understand the topology file format. It is essential that you understand exactly how it works and what is going on or else you are more likely to have errors in your simulation. I am h

Re: [gmx-users] How to modify H atom type from opls_369 to match H expected by popc.itp

Quoting sudheer babu <[EMAIL PROTECTED]>: > Hi all, > Two days back I posted this question, no one replied thats why I am posting > again. It is typically advisable to not post the same question multiple times until you get an answer. Try to solve your issue on your own and report back with what

Re: [gmx-users] Please let me know where can I found parameters for Phosphorylated amino acids.

Quoting SeungPyo Hong <[EMAIL PROTECTED]>: > Dear gmx-users, > > I want to perform MD with or withou phosphorylated proteins and to compare > their differences. > Because the phosphorylation is well known phenomena, I guess there some of > you had done MD with it. > I will be glad if you let me kn

Re: [gmx-users] how can I restart simulation

Quoting Anamika Awasthi <[EMAIL PROTECTED]>: > Dear Gromacs Users, > I have done MD simulation for 15 ns and I need simulation for further > 5 ns. > I am wondering how is this possible? http://wiki.gromacs.org/index.php/Doing_Restarts This question is often asked; check the archive b

[gmx-users] how can I restart simulation

Dear Gromacs Users, I have done MD simulation for 15 ns and I need simulation for further 5 ns. I am wondering how is this possible? Thank you in advance Anamika ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mai

Re: [gmx-users] problem with bilayer PBC. after dynamics, bilayer becomes 2 monolayers (shift in box center?)

It sounds like you have it pretty clear already. A point to note, in GROMACS the origin coordinate 0,0,0 is at a corner of the box, not the centre. This could be what caused such a big (apparent) shift. - Original Message From: maria goranovic <[EMAIL PROTECTED]> To: Discussion list

[gmx-users] problem with bilayer PBC. after dynamics, bilayer becomes 2 monolayers (shift in box center?)

Hello Folks, I am simulations a lipid bilayer. After minimization, the output .gro file contains a bilayer that is a layer of water sandwiched between 2 monolayers of lipids (instead of being the other way around). I guess this has something to do with the periodic shift in boxes or something. Can

Re: [gmx-users] Simulation at different temperature

different mdp files with different ref_t. Regards, Yang Ye - Original Message From: s lal badshah <[EMAIL PROTECTED]> To: gromacs Sent: Monday, March 31, 2008 12:48:47 PM Subject: [gmx-users] Simulation at different temperature Dear Experts, Hi ! I want to simulate a protein at 298K,

[gmx-users] Please let me know where can I found parameters for Phosphorylated amino acids.

Dear gmx-users, I want to perform MD with or withou phosphorylated proteins and to compare their differences. Because the phosphorylation is well known phenomena, I guess there some of you had done MD with it. I will be glad if you let me know where can I found reliable parametered, or residue top