RE: [gmx-users] wants to simulate for more timesteps

Hi, You may try "tpbconv". Read help for "tpbconv" first. Siavoush From: [EMAIL PROTECTED] on behalf of Anamika Awasthi Sent: Thu 2008/03/20 08:14 ق.ظ To: gmx-users@gromacs.org Subject: [gmx-users] wants to simulate for more timesteps Dear Gromacs Users, I h

[gmx-users] wants to simulate for more timesteps

Dear Gromacs Users, I have simulated my protein for 15 ns, I need to simulate it for more. How can I do this? Is this any easy way that it can restart after previous 15 ns? Thanks in advance -- Anamika Awasthi, PhD DBT-Postdoctoral Fellow Laboratory of Structural Biology Centre for DNA

[gmx-users] tutorial for membrane-bound systems

Dear all, I would like to make MD simulations of a drug at the binding site of the receptor sorrounded by DPPC. pdb coordinate file of all DPPC units (189 units, 1 unit has 130 atoms) are described seperately. I was using Dundee PRODRG server for generating .itp and drgpoh2.pdb files for

[gmx-users] construct electron density from file WANNIER_CENTER

Dear all, I am simulating a system with Gromacs/CPMD and have the output files WC_SPREAD and WANNIER_CENTER from CPMD. Now I need construct the electron density from them. Would some one please tell me how to do that? Thanks a lot in advance. The following is the content of file WC_SPREAD:

Re: [gmx-users] pdb2gmx error

Quoting Gadzikano Munyuki <[EMAIL PROTECTED]>: > I want to do dynamics on a cyclic polypeptide. The peptide contains a residue > that is not standard Ornithine. I have added [ORN] to the ffoplsaa.rtp file > and the aminoacids.dat file.I have put these in the working directory and > also in the lib

Re: [gmx-users] pdb2gmx error

No, but you should try to distinguish an O (letter-O) from a 0 (numeric zero). Tsjerk On Wed, Mar 19, 2008 at 3:54 PM, Gadzikano Munyuki <[EMAIL PROTECTED]> wrote: > I want to do dynamics on a cyclic polypeptide. The peptide contains a residue > that is not standard Ornithine. I have added [ORN]

[gmx-users] pdb2gmx error

I want to do dynamics on a cyclic polypeptide. The peptide contains a residue that is not standard Ornithine. I have added [ORN] to the ffoplsaa.rtp file and the aminoacids.dat file.I have put these in the working directory and also in the library. If I grep these files [ORN] is there but i stil

Re: [gmx-users] How to create three different zones to minimize energy of a enzyme?

I suppose it should be mentioned that even with an average desktop computer it should be more than feasible to minimise the whole of your enzyme system. If you want to simulate the system for long periods of time then that is a different question. Tom --On Wednesday, March 19, 2008 08:34:29 +

RE: [gmx-users] SGI installation problem

Hi, Thanks for the suggestion and I am sorry that didn't let the list know that the problem had been fixed. (I haven't used the mdrun yet, but the other stuff seems working) Thanks to the Makefile that I have received from David. I compared that file with the one created in the script director

[gmx-users] Black whole simluations

Deear mister Ben, I don't know if your mail is serious, however I find your system very interesting. Personally we think you mail might be joke, however I will do besst I can do helping you. My professor had once similar good idea. We are currently implementing relativist

Re: [gmx-users] center of mass removal

Tsjerk Wassenaar wrote: Hi [EMAIL PROTECTED], I have recently modified the routine as to not crash upon a shift over periodic boundaries, which would occur with the original code. Also, I streamlined the routines such that they don't lead to large modifications of update.c I will put the modifie

Re: [gmx-users] configure error (lam-mpi installation)

Andreas Kring wrote: Hi all. I have tried to search the mailing archives and the FAQ, but I could not find an answer, so here goes... This is not surprising, since your problem is with configuring LAM, not GROMACS. Actually, the reason for your problem not dependent on the software you're t

Re: [gmx-users] complete energy minimization

Justin A. Lemkul wrote: Quoting s lal badshah <[EMAIL PROTECTED]>: Dear experts, Hi! I minimized the system and gies 10,000 nsteps, but the output is: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 1000. Potential Energy = -1.9742134e+21 M

[gmx-users] configure error (lam-mpi installation)

Hi all. I have tried to search the mailing archives and the FAQ, but I could not find an answer, so here goes... I'm using Ubuntu 7.10 and the latest gcc compiler in this distro is gcc-4.1.2. Being aware of the warning that the gcc-4.1.x compilers are broken, I installed gcc-4.3.0 using the

Re: [gmx-users] complete energy minimization

Quoting s lal badshah <[EMAIL PROTECTED]>: > Dear experts, > Hi! I minimized the system and gies 10,000 nsteps, but the output is: > > Steepest Descents converged to machine precision in 15 steps, > but did not reach the requested Fmax < 1000. > Potential Energy = -1.9742134e+21 > Maximum force

[gmx-users] complete energy minimization

Dear experts, Hi! I minimized the system and gies 10,000 nsteps, but the output is: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 1000. Potential Energy = -1.9742134e+21 Maximum force = 4.1648520e+06 on atom 1934 Norm of force = 5.6

Re: [gmx-users] SGI installation problem

Hi, I'm not quite sure what David was thinking, but Makefiles are created on-the-fly with automake/autoconf and tailored to the commands on your system, so there is absolutely no way a Mac makefile will work on an SGI :-) An error like make: file 'Makefile' line 417: syntax error *** Err

RE: [gmx-users] Remove COM of group only in x & y direction

Hi, Not in version 3.3. In version 4.0 only x & y will be selected automatically when there are walls along z-planes. Berk. > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Date: Tue, 18 Mar 2008 22:14:20 -0600 > Subject: [gmx-users] Remove COM of group only in x & y direction > > He

Re: [gmx-users] g_anaeig

> thanks for the help... > sorry I made a mistake with flags -f -e in the mail Right, well there's a lesson for you. Computers are literal, and so tend to be the people who use them well. Copy-and-paste helps you to be literal. Filtering things through your head tends to increase errors. Mark >

Re: [gmx-users] center of mass removal

Hi [EMAIL PROTECTED], I have recently modified the routine as to not crash upon a shift over periodic boundaries, which would occur with the original code. Also, I streamlined the routines such that they don't lead to large modifications of update.c I will put the modified code on line, probably t

Re: [gmx-users] g_anaeig

thanks for the help... sorry I made a mistake with flags -f -e in the mail Swapna On Tue, Mar 18, 2008 at 4:43 PM, Mark Abraham <[EMAIL PROTECTED]> wrote: > SWAPNA wrote: > > Dear gmx users, > > I am using g_anaeig to filter my traj along the first eigenvector. > > > > 'g_anaeig -b 5000 -f 15000

Re: [gmx-users] How to create three different zones to minimize energy of a enzyme?

Hi Lacerda, You should be cautious in the interpretation of your results. Your active site will only be minimized in potential energy in the context of your frozen surface and your restraint internal degrees of freedom. You should be very confident that your surface is about correct and your inter