[gmx-users] reagrding huggins meyer potential

Dear all, I wanted to simulate Nacl in water using huggins meyer potential as vdw type.since gromacs has just LJ OR BJ potential i wanted to know if somebody had done it with huggins meyer potential.I read the manual and since i am not good in c or fortran i dono how to create a user

Re: [gmx-users] compilation instructions, the gromacs wiki, documentation, and test suites

Chris, sorry I didn't pay attention (was in a hurry). I know that you have helped with the documentation and wouldn't have suggested to you to put it on the wiki if I recognized it was you. I thought it was a new user. And I didn't want to criticize but only point out (to the assumed new user) tha

Re: [gmx-users] Question regarding g_rdf

rainy...@yahoo.com wrote: Hello, I am fairly new to using Gromacs and am writing to seek clarification on the g_rdf module. In the manual, it states that "g_rdf calculates radial distribution functions in different ways. The normal method is around a (set of) particle(s), the other method

[gmx-users] Question regarding g_rdf

Hello, I am fairly new to using Gromacs and am writing to seek clarification on the g_rdf module. In the manual, it states that "g_rdf calculates radial distribution functions in different ways. The normal method is around a (set of) particle(s), the other method is around the center of mass of a

[gmx-users] compilation instructions, the gromacs wiki, documentation, and test suites

<"cmake --> relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object;>> Dear Roland: It is not my intention to be confrontational, your assistance was very useful, I appreciate it very much, and I realize that it's not your job to comment everything (or

Re: [gmx-users] cmake --> relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object;

e/intel/fftw-3.1.2_again/exec/lib/ >>> libfftw3f.la: >>> file not recognized: File format not recognized >>> >>> USING -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/ >>> libfftw3f_th

[gmx-users] cmake --> relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object;

ORNL PO BOX 2008 MS6309 -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20101220/a6a71aac/attachment.html -- -- gmx-users mailing list gmx-users@gromacs.org http://list

Re: [gmx-users] how to add a electric field to the water box when do a simulation

On 21/12/2010 3:39 AM, Daniel P. Luis J. wrote: I think you would to try 1 10.0 0.0. In the numbers, GROMACS does not determine whether to store an input number as an integer or a float based on the presence of numbers after a decimal point. The range of permissible values determines the data

Re: [gmx-users] cmake --> relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object; recompile with -fPIC

You want to compile fftw with either --enable-shared or with --with-pic. Or you need to compile a static version of Gromacs. As the message says you can't use fftw without pic with shared libraries in GROMACS. Roland On Mon, Dec 20, 2010 at 6:31 PM, Chris Neale wrote: > Dear Gromacs users: > > I

[gmx-users] cmake --> relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object; recompile with -fPIC

Dear Gromacs users: I pulled the master version of the source code today at 2pm via: git clone git://git.gromacs.org/gromacs.git and I tried to compile it following the instructions posted here: http://www.gromacs.org/Developer_Zone/Cmake but I was unsuccessful. This is my first attempt at usi

Re: [gmx-users] how to add a electric field to the water box when do a simulation

I think you would to try 1 10.0 0.0. In the numbers, On Mon Dec 20th, 2010 3:59 AM PST Carsten Kutzner wrote: >On Dec 20, 2010, at 12:09 PM, 松啸天 wrote: > >> dear: >>I would like to use the electric field inside a box defined by gromacs. >> So I added E_x 1 10 0in the .mdp file, is it the

Re: [gmx-users] how to add a electric field to the water box when do a simulation

On Dec 20, 2010, at 12:09 PM, 松啸天 wrote: > dear: >I would like to use the electric field inside a box defined by gromacs. > So I added E_x 1 10 0in the .mdp file, is it the right approach? Yes, this will add an electric field of strength 10 V/nm acting in x-direction. Carsten > i hope p

[gmx-users] Reg: Dihedral conversion from fourier to RB form

Hi all I want to convert the fourier co-efficients into RB form.i have V1, V2 and V3 in the literature. My question is V1,V2 and V3 corresponds to F1,F2 and F3 in the manual?. I just want to confirm one more thing to convert fourier coefficients to RB form the formula i have to use is 4.64 in the

[gmx-users] search for help

dear: I would like to use the electric field inside a box defined by gromacs. So I added E_x 1 10 0 in the .mdp file, is it the right approach? i hope people who knows will help me to add the electric field when i do a simulation.that's all.thank you! yours

[gmx-users] how to add a electric field to the water box when do a simulation

dear: I would like to use the electric field inside a box defined by gromacs. So I added E_x 1 10 0 in the .mdp file, is it the right approach? i hope people who knows will help me to add the electric field when i do a simulation.that's all.thank you! yours

Re: [gmx-users] Reg: fatal error pdb2gmx

On 20/12/2010 4:25 PM, vinothkumar mohanakrishnan wrote: Hi all I want to use pdb2gmx to generate hexane topology and hexane.gro file. i have added the atom name in .atp file and corresponding section in .rtp file. i have given below my .rtp entry You don't need to add an .rtp entry, it's as

Re: [gmx-users] reagarding polarisable force field in gromacs

On 20/12/2010 3:44 PM, sreelakshmi ramesh wrote: Dear justin , I am using tip4p water model for my work and i have the tip4p.itp file if i just wanted polarisable force field so as you told me i have the tip4p.itp file.should i modify this file or the force field.itp file