[gmx-users] Setting up an infinitely hard wall

2009-10-22 Thread Amit Choubey
Hi everyone, I am sending this email again hoping for any quick input for my question. I have been trying to set up an "infinitely" hard potential wall. I tried to use the available wall options and could not really get it to do what i needed. I wanted a steep repulsive potential but when i cr

Re: [gmx-users] POPG-Martini Force Field

2009-10-22 Thread Amit Choubey
On Thu, Oct 22, 2009 at 9:53 AM, S hv wrote: > Hi, > > I am currently working with peptide/lipids interactions using the martini > force field. I want to built a bacterial membrane, so I trying to find the > topology of the POPG lipid but until now without success. > > > In the martini_v2.0_li

Re: [gmx-users] Diffusion coefficient depenting on time interval

2009-10-22 Thread David van der Spoel
Erik Marklund wrote: Hi users, I have simulated a box of NVT-water, more specifically the flexible urey-bradley-like TIPS-reparametrisation by Dang and Pettitt (1987). What I notice is that the diffusion coefficient increases when I calculate it from a longer snippet from my trajectory. If I

Re: [gmx-users] how to mimick explicit hydrogen bonding

2009-10-22 Thread ms
Mark Abraham ha scritto: > ms wrote: >> Ok, the problem is that I want to re-implement a quite minimal >> coarse-grained FF (so no explicit solvent etc.) and a directional >> interaction would be useful. > > Well you should consider alternative software, then. I see. I wonder if patching gmx to d

[gmx-users] POPG-Martini Force Field

2009-10-22 Thread S hv
Hi, I am currently working with peptide/lipids interactions using the martini force field. I want to built a bacterial membrane, so I trying to find the topology of the POPG lipid but until now without success. In the martini_v2.0_lipids.itp file, the PG lipids are no included. I have seen

[gmx-users] PMF and g_wham

2009-10-22 Thread Stefan Hoorman
While using g_wham to obtain a PMF from umbrella sampling simulations I came up with the following problem. I have simulated my windows with a 0.1nm difference between structures starting from the initial position where my dimer is equilibrated and ending 0.5nm farther than what the lennard jones a

[gmx-users] gromacs 4.0.4 on BG/P performance

2009-10-22 Thread Peicho Pektov
Hello, I've compiled gromacs on BlueGene/P system and it would be great if some one send me an input and tell me what is the performance of the gromacs runing this job on another BG/P system. Thank you in advance! Peicho. ___ gmx-users mailing list

[gmx-users] Diffusion coefficient depenting on time interval

2009-10-22 Thread Erik Marklund
Hi users, I have simulated a box of NVT-water, more specifically the flexible urey-bradley-like TIPS-reparametrisation by Dang and Pettitt (1987). What I notice is that the diffusion coefficient increases when I calculate it from a longer snippet from my trajectory. If I use only 100 ps; star

[gmx-users] free energy cycle and couple-intramol setting

2009-10-22 Thread Elio Cino
Hello. I am working on some free energy calculations for a protein-protein interaction. I decided to try and reproduce the delta G for the well-studied barnase-barstar interaction before I work with a novel system. I am running the FE calculations on the barnase-barstar complex, and the barnase

[gmx-users] converting itp/pdb file to FIELD file

2009-10-22 Thread Jamie Seyed
Dear Gmx users, Does any one know how to convert itp/pdb file to dlpoly FIELD format?? Any information regarding that will really appreciate... Please let me know if you have any reference/script ... to make my FIELD file for dlpoly since I am trying that for a while... Many Thanks in Advance/Jamie

[gmx-users] Re: COM removal type angular with PBC?

2009-10-22 Thread jennifer johnston
>1. Re: COM removal type angular with PBC? (Mark Abraham) >> Dear All, >> I'm attempting to simulate a dimeric protein in an explicit >> bilayer/water environment. I'd like to remove the translation & rotation >> of one protomer relative to the other, so that one protomer is able to >>

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

2009-10-22 Thread Mark Abraham
ram bio wrote: Dear Mark, Thanks and you are right, that when a docked complex (protein + ligand) is simulated, the favorable ligand binding poses can be predicted using MD (longer runs). What I am trying to do here presently is not to simulate a docked complex, but to generate a modelled protei

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

2009-10-22 Thread ram bio
Dear Mark, Thanks and you are right, that when a docked complex (protein + ligand) is simulated, the favorable ligand binding poses can be predicted using MD (longer runs). What I am trying to do here presently is not to simulate a docked complex, but to generate a modelled protein lowest energy c

Re: [gmx-users] Re: converting proper dihedrals into ryckaert-bellemans

2009-10-22 Thread Mark Abraham
Carla Jamous wrote: Dear Alan, if I completely understood how acpypi works, it seems that it generates the topology parameters from the pdb file of the molecule. But the problem is that I have the topology parameters (my angles, bond distances and dihedrals) and want to implement them in Gromac

Re: [gmx-users] Re: converting proper dihedrals into ryckaert-bellemans

2009-10-22 Thread Carla Jamous
Dear Alan, if I completely understood how acpypi works, it seems that it generates the topology parameters from the pdb file of the molecule. But the problem is that I have the topology parameters (my angles, bond distances and dihedrals) and want to implement them in Gromacs, so actually I want to

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

2009-10-22 Thread Mark Abraham
ram bio wrote: Dear Mark, You mean that I should consider a configuration with the lowest total energy for docking studies..Please clarify and suggest me. If you read your docking program's documentation, they are using their "energy" as a some kind of approximation to a free energy of ligand

RE: [gmx-users] g_rdf and number of atoms to include

2009-10-22 Thread Enemark Soeren
Thanks Mark and Omer for your comments - I have really learning a lot on RDF today based on your input! From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Omer Markovitch Sent: Thursday, October 22, 2009 3:49 PM To: Discussion list for GROMACS users Subj

Re: [gmx-users] time steps and segmentation fault

2009-10-22 Thread XAvier Periole
On Oct 22, 2009, at 11:54 AM, albita...@virgilio.it wrote: Hi, I'm checking my system and topology but I noticed a quite weird behaviour in this concern. When I run my simulation starting from a pre-optimized geometry, the simulation crashes with segmentation fault. what do you mean by p

Re: [gmx-users] time steps and segmentation fault

2009-10-22 Thread albita...@virgilio.it
Hi, I'm checking my system and topology but I noticed a quite weird behaviour in this concern. When I run my simulation starting from a pre-optimized geometry, the simulation crashes with segmentation fault. On the other hand, when I run the same simulation but starting from the geometry I generate

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

2009-10-22 Thread ram bio
Dear Mark, You mean that I should consider a configuration with the lowest total energy for docking studies..Please clarify and suggest me. Thanks, Ram On Thu, Oct 22, 2009 at 3:56 AM, Mark Abraham wrote: > ram bio wrote: >> >> Dear Justin, >> >> Thanks for the suggestion and advice. >> As i h

Re: [gmx-users] RE: No default G96 Bond types error

2009-10-22 Thread Mark Abraham
Kukol, Andreas wrote: Hi, Finally I found the reason for the error: A space is required between the forcefield parameter code and the semicolon indicating a comment, i.e.: No default G96Bond types error: 3132 2gb_18; C-O ether bond <- line 88 Works fine: 3132 2

[gmx-users] RE: No default G96 Bond types error

2009-10-22 Thread Kukol, Andreas
Hi, Finally I found the reason for the error: A space is required between the forcefield parameter code and the semicolon indicating a comment, i.e.: No default G96Bond types error: >3132 2gb_18; C-O ether bond <- line 88 Works fine: >3132 2gb_18 ; C-O ether bo

Re: [gmx-users] g_rdf and number of atoms to include

2009-10-22 Thread Omer Markovitch
On Thu, Oct 22, 2009 at 05:17, Enemark Soeren wrote: > Ahh, now I understand - sorry, Omer! > > No problem, glad to help. > > > In fact, I have compared all three single hydrogen RDFs and they are > identical and also relatively smooth. Since, however, with 3 times more data > points (all thre