Re: [gmx-users] (no subject)

2014-02-28 Thread Justin Lemkul
On 2/28/14, 5:38 AM, abhijit Kayal wrote: Dear Gromacs users, My system contained CNT+ water. I have created a dynamically index.ndx file which contain the number of water molecules in each frame inside cnt. Now I want to study the dipole orientation of these water molecules. But I

Re: [gmx-users] (no subject)

2014-02-28 Thread abhijit Kayal
Thanks Justin for the help. But if I want to look the dipole auto correlation or hydrogen bond dynamics ... is that possible? On Fri, Feb 28, 2014 at 4:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/28/14, 5:38 AM, abhijit Kayal wrote: Dear Gromacs users, My system contained

Re: [gmx-users] (no subject)

2014-02-28 Thread Justin Lemkul
On 2/28/14, 6:36 AM, abhijit Kayal wrote: Thanks Justin for the help. But if I want to look the dipole auto correlation or hydrogen bond dynamics ... is that possible? Each frame is just a time point in the trajectory. Concatenate the individual output and you get a time series. -Justin

[gmx-users] Can i use GPU for my desktop computer

2014-02-28 Thread xiao
Dear GMX users, I learned that GPU can acceleprate the speed of MD, but i do not know whether it is possible to use GPU on desktop. Our Lab does not have supercomputer, and i can only run gromacs by using normal comuters. The computer i am using is hp，and it has 8 i7 cores. Whan kind of GPU

[gmx-users] ref_t and gen_temp

2014-02-28 Thread Turgay Cakmak
Hi all, I want to run some simulations at different temperatures (protein and solvent) changing the ref_t values. First at 300K, then 320K so on.. So, my question is: should I also change the gen_temp value while changing the ref_t value? Thanks and regards, Turgay -- Gromacs Users

Re: [gmx-users] ref_t and gen_temp

2014-02-28 Thread Justin Lemkul
On 2/28/14, 10:21 AM, Turgay Cakmak wrote: Hi all, I want to run some simulations at different temperatures (protein and solvent) changing the ref_t values. First at 300K, then 320K so on.. So, my question is: should I also change the gen_temp value while changing the ref_t value? Yes.

[gmx-users] xpm2ps

2014-02-28 Thread Nidhi Katyal
Hello, I would like to change the scale of x axis and y axis of my dssp.eps file by different amounts. Example with xpm2ps -skip command I can write out every nr-th row and nr-th column but I want every nr-th row and mr-th column. Please suggest if it is possible to do so. Thanks in advance.

[gmx-users] PME

2014-02-28 Thread kiana moghaddam
Dear GMX users I run gromacs 4.6.3 in parallel for my system. My simulation box is triclinic. My MD simulation is computed on in-house Linux 64-bit Intel Core-i7.  As far as I know, for triclinic box, the optimal setup will have a PME load of 0.25, so I change pme order and grid spacing in my

Re: [gmx-users] xpm2ps

2014-02-28 Thread David van der Spoel
On 2014-02-28 16:39, Nidhi Katyal wrote: Hello, I would like to change the scale of x axis and y axis of my dssp.eps file by different amounts. Example with xpm2ps -skip command I can write out every nr-th row and nr-th column but I want every nr-th row and mr-th column. Please suggest if it is

[gmx-users] A question about blowing up

2014-02-28 Thread sujithkakkat .
Hello, I am following justin lemkul's tutorials for the cyclohexane-water biphasic system using Gromos96 forcefield. Things went well till NVT equilibration where I had this Blowing up issue. Shortening the time step alone did not help, and it was difficult for me to figure out what was