[gmx-users] how to use the new potential

>He, Yang wrote: >> Hi all users, >> >> I am engaged in deal with the course grain model,in which the >> potential functions are not the same as in gromacs.Hence, If I want to >> use the new potentials , I guess I can change the source code or use >> the table. But I never have this experienc

[gmx-users] nematic phase disappears with reducing the time step

hi, i am doing simulations NVT simulations of rigid charged rods (with constrained bonds and stiff bending potential)in vacuum using PME for the electrostatics with a time step of 0.0015 ps (which i think is a pretty reasonable value for a corse grain model) A nematic phase of the rods appears

[gmx-users] Smallest allowed cell size

Hi, I received the following error --- Program mdrun, VERSION 4.0 Source code file: domdec.c, line: 2933 Fatal error: Step 10: The X-size (-32.295326) times the triclinic skew factor (1.00) is smaller than the smallest allowed cell size (1.

Re: [gmx-users] g_rotacf

How should I change it so it calculates the 40 ps? On Wed, Oct 22, 2008 at 6:34 PM, Xavier Periole <[EMAIL PROTECTED]> wrote: > On Wed, 22 Oct 2008 17:38:58 -0400 > "Daniel K" <[EMAIL PROTECTED]> wrote: > >> I have been trying to use g_rotacf with a simulation run for 40 ps (2) >> with steps

[gmx-users] m) Re: modify bondfree.c and recompile

Hi Berk and Mark, Thank you all for the suggestions. I will follow the safe way (make under src or top-level dir). > Date: Thu, 23 Oct 2008 02:29:14 +1100 > From: Mark Abraham <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Re: modify bondfree.c and recompile > To: Discussion list for GROMACS user

Re: [gmx-users] g_rotacf

On Wed, 22 Oct 2008 17:38:58 -0400 "Daniel K" <[EMAIL PROTECTED]> wrote: I have been trying to use g_rotacf with a simulation run for 40 ps (2) with steps of 2fs and the frames where extracted every 50 fs (25 frames). The trajectory file is correct because it has 801 frames. When I calculate

[gmx-users] g_rotacf

I have been trying to use g_rotacf with a simulation run for 40 ps (2) with steps of 2fs and the frames where extracted every 50 fs (25 frames). The trajectory file is correct because it has 801 frames. When I calculate the g_rotacf I only get 20 ps and the time step is 50 fs. Does any body no

Re: [gmx-users] How to make a pdb file for methane pair?

Hi, Justin: I put a residue name ( ALA) there, but pdb2gmx told me that there is a fatal error: Atom H4 in residue ALA 1 not found in rtp entry with 6 atoms while sorting atoms. Maybe different protonation state. Remove this hydrogen or choose a different protonation stat

[gmx-users] Setting constant velocity

Is there a way to set a constant velocity to simulate fluid flow? I know I can apply a force to increase velocity, but can I keep the velocity constant after that? Thanks, Andy ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/ma

Re: [gmx-users] spliting clusters.pdb

Abu Naser wrote: > Hi All, > > I have been wondering whether there is any tools for spliting clusters.pdb > file into individual snapshots. If there is a TER between the structures, the shell command csplit may be useful for you. Jochen > > With regards, > > Abu > > > > > > > > _

Re: [gmx-users] How to make a pdb file for methane pair?

xianghong qi wrote: Hi, Justin: I put a residue name ( ALA) there, but pdb2gmx told me that there is a fatal error: Atom H4 in residue ALA 1 not found in rtp entry with 6 atoms while sorting atoms. Maybe different protonation state. Remove this hydrogen or choose a

Re: [gmx-users] how to use the new potential

He, Yang wrote: Hi all users, I am engaged in deal with the course grain model,in which the potential functions are not the same as in gromacs.Hence, If I want to use the new potentials , I guess I can change the source code or use the table. But I never have this experience about that.Can a

Re: [gmx-users] Re: modify bondfree.c and recompile

Jian Zou wrote: Hi Mark, David and Bess, Thank you all for the suggestions. I know the dependency has to be somewhere in the Makefiles or the files they include but I cannot find it. What I am doing is simply "make" under top-level source directory followed by make install. In this case, the c

Re: [gmx-users] monomer's conectivity

Andrea Muntean wrote: I have a *pdb file for a polymer box which I want to use. I defined the residues (the first, the last and the inner monomers). Pdb2gmx runs, but I obtain a "soup" of monomers instead of N chains a M monomers each. My problem now is how to connect the monomers. What is the b

Re: [gmx-users] modify bondfree.c and recompile

He, Yang wrote: Hi David, Thank you for your reply. As for the new non-bond potential, if I want to use the gromacs to deal with them, what should i do in the gromacs? Do you have any suggestions about that? Change the source code? You can use tables for bonded potentials as well, without

[gmx-users] how to use the new potential

Hi all users, I am engaged in deal with the course grain model,in which the potential functions are not the same as in gromacs.Hence, If I want to use the new potentials , I guess I can change the source code or use the table. But I never have this experience about that.Can anyone of you give

[gmx-users] monomer's conectivity

I have a *pdb file for a polymer box which I want to use. I defined the residues (the first, the last and the inner monomers). Pdb2gmx runs, but I obtain a "soup" of monomers instead of N chains a M monomers each. My problem now is how to connect the monomers. What is the best way to do so? Regard

RE: [gmx-users] Re: modify bondfree.c and recompile

Hi, In the Makefiles in kernel, tools and ngmx you will see that all binaries depend on gmxlib and mdlib. So if you type make in the top level directory or in src/kernel, first bondfree.c will be compiled and put into the gmxlib library, in kernel make will then notice that gmxlib is new and relin

[gmx-users] Re: modify bondfree.c and recompile

Hi Mark, David and Bess, Thank you all for the suggestions. I know the dependency has to be somewhere in the Makefiles or the files they include but I cannot find it. What I am doing is simply "make" under top-level source directory followed by make install. In this case, the content of all the

Re: [gmx-users] How to make a pdb file for methane pair?

Thanks so much , Justin. I will try. -Xianghong Qi On Wed, Oct 22, 2008 at 7:41 AM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > xianghong qi wrote: > >> Thanks, so how to edit a residue name ? I am confused. sorry about such >> simple question. >> > > Use a text editor. Be sure to keep t

RE: [gmx-users] modify bondfree.c and recompile

Hi David, Thank you for your reply. As for the new non-bond potential, if I want to use the gromacs to deal with them, what should i do in the gromacs? Do you have any suggestions about that? Change the source code? Thank you for your help. Regard, Yang __

Re: [gmx-users] spliting clusters.pdb

Abu Naser wrote: Thanks Justin. I did try and did not work. trajconv is more of controlled by time step. It works just fine for me when I've got a clusters.pdb file; what command did you try? -Justin With regards, Abu > Date: Wed, 22 Oct 2008 08:59:39 -0400 > From: [EMAIL P

Re: [gmx-users] spliting clusters.pdb

Abu Naser wrote: Hi All, I have been wondering whether there is any tools for spliting clusters.pdb file into individual snapshots. Try: trjconv -sep -Justin With regards, Abu Read amazing stories to you

[gmx-users] spliting clusters.pdb

Hi All, I have been wondering whether there is any tools for spliting clusters.pdb file into individual snapshots. With regards, Abu _ Win an Xbox 360 or £200 Top Shop Vouchers http://clk.atdmt.com/GBL/go/115454062/dir

Re: [gmx-users] How to make a pdb file for methane pair?

xianghong qi wrote: Thanks, so how to edit a residue name ? I am confused. sorry about such simple question. Use a text editor. Be sure to keep the formatting right when doing so: http://www.wwpdb.org/documentation/format32/sect9.html -Justin -Xianghong Qi On Tue, Oct 21, 2008 at 9:0

Re: [gmx-users] How to make a pdb file for methane pair?

Thanks, so how to edit a residue name ? I am confused. sorry about such simple question. -Xianghong Qi On Tue, Oct 21, 2008 at 9:01 PM, Mark Abraham <[EMAIL PROTECTED]>wrote: > xianghong qi wrote: > >> Hello, everyone, >> I want to create a pdb file for methane pair . I can make methane pair >>

RE: [gmx-users] Walls & user defined potential

Date: Wed, 22 Oct 2008 05:55:16 +0800 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] Walls & user defined potential Hi gmx-users and developers, I met a strange error when using wall function combined with user defined potential. Following is a part of the mdp: ---

[gmx-users] RE: How can I generate a Input *.gro file of coarse grain(xuji)

Hi Yang: I checked the potential fnctions the Martini force field used in Gromacs. The bond and angle potential funtions are g96 harmonic potential functions. The VDW and COULOMB potential functions are in nb_kernel330_x86_64_sse.s file in my workstation's environment. >Hi , > >I was also engage

RE: [gmx-users] How to make a soft repulsive potential wall

Date: Wed, 22 Oct 2008 01:22:09 +0800 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] How to make a soft repulsive potential wall Hi gmx-users, I was simulating a water-surface system recently. The water molecules will escape from the solid surface, evaporate into the