[gmx-users] Invalid line in coordinate file (grompp tool)

2013-10-02 Thread Andrew Bostick
Dear users, I have used grompp command for minimising my system (protein and membrane). I am getting the error: --- Program grompp, VERSION 4.5.1 Source code file: confio.c, line: 744 Fatal error: Invalid line in system.gro for atom 11380: 6

Re: [gmx-users] Invalid line in coordinate file (grompp tool)

2013-10-02 Thread Justin Lemkul
On 10/2/13 8:21 AM, Andrew Bostick wrote: Dear users, I have used grompp command for minimising my system (protein and membrane). I am getting the error: --- Program grompp, VERSION 4.5.1 Source code file: confio.c, line: 744 Fatal error: I

[gmx-users] Invalid line in coordinate file (grompp tool)

2013-10-02 Thread Andrew Bostick
Dear Justin Thanks for your quick reply. What is reason of this issue? My gro file contains 11383 lines. 11383-3=11380 This value is equal to second line. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at htt

Re: [gmx-users] Invalid line in coordinate file (grompp tool)

2013-10-02 Thread Justin Lemkul
On 10/2/13 8:45 AM, Andrew Bostick wrote: Dear Justin Thanks for your quick reply. What is reason of this issue? My gro file contains 11383 lines. 11383-3=11380 This value is equal to second line. Sorry, misread your initial post. One of two things is happening: 1. You've used an edit

[gmx-users] Problem running free energy simulations

2013-10-02 Thread Jernej Zidar
Hi all, I'm trying to determine the free energy of solvation for a molecule in n-octanol. I'm separately turning off the Coulomb and Lennard-Jones interactions as instructed in the free energy tutorial. The Lennard-Jones simulations keep on crashing for most values of lambda with the message: Pro

Re: [gmx-users] Problem running free energy simulations

2013-10-02 Thread Michael Shirts
Sounds like the simulation is blowing up. How soon does it start crashing. Also, what configurations are you using to start your free energy simulations at each lambda? On Wed, Oct 2, 2013 at 10:31 PM, Jernej Zidar wrote: > Hi all, > I'm trying to determine the free energy of solvation for a

[gmx-users] (no subject)

2013-10-02 Thread prithvi raj pandey
Dear gmx-users, We intend to perform free energy calculations by pulling a polypeptide along water-hexane interface. We need to pull the polypypeptide from the water layer towards the hexane layer (crossing the interface). For this we position restrained one hexane molecule in the bulk of hexane (