[gmx-users] How to check whether GROMACS was installed correctly?

Hello I have installed GROMACS 3.3.1 for the first time and want to check whether it was done correct or not. There were no error messages during installation but when it was done I typed: $./luck there was error message something like 'Command not found' Maybe installation was wrong anyw

Re: [gmx-users] Segmentation error (core dump)

The problem was resolved after reinstall cygwin and gromacs. Thanks. - Original Message - From: "Mark Abraham" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Sent: Sunday, January 14, 2007 5:31 PM Subject: Re: [gmx-users] Segmentation error (core dump) > Dear gmx-users, > >

Re: Re: [gmx-users] infinitive force acting on atom during

Dear Tsjerk, dear gromacs-users and developers, thank you for your kind help and information about my problem. However, the atom "atom 2005" (see below) which feels an infinitive force acting on it is a water molecule which is not in the original pdb file which I used for my simulations. So I

Re: Re: [gmx-users] infinitive force acting on atom during

Hi Joern, In any case, you want to first perform an energy minimization in vacuum to release the strain present in your starting structure. Only then can you be sure that if you run into trouble after solvating your system, it is caused by that. It may be that during solvation a solvent molecule

RE: Re: [gmx-users] infinitive force acting on atom during

Dear all, I run the NPT (anisotropic) for the urea-water system. After the md run the pressure is not closer to 1 bar but in terms of 100. Suggest me the corrections in my parameter file. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Tsjerk Wassenaar S

Re: [gmx-users] infinitive force acting on atom during

Sivashangari Gnanasambandam wrote: Dear all, I run the NPT (anisotropic) for the urea-water system. After the md run the pressure is not closer to 1 bar but in terms of 100. Suggest me the corrections in my parameter file. When you post to this list, please use a Subject for your email that i

[gmx-users] How to run NPT (anisotropic simulatio) for urea-water system with variable axis only in z direction

Hi, I am trying to study the dissolution of urea in water. After adding the water molecule using genbox, I did the energy minimization by applying pbc. Then I run the equilibration for 300ps using NPT anisotropic pressure coulpling and variable axis only in the z direction. The reference pressure

Re: Re: [gmx-users] error while compilation of Gromacs 3.3.1.....

Dear Dr. Martin Hoefling, Thankyou for the reply. I have installed the gromacs 3.3 package on my PC with gcc compilers and I didnot get any such errors. I am using the package with any hitch. Any other information you would like me to give in this regard kindly let m