Re: [gmx-users] g_tcaf segmentation fault

2012-09-27 Thread Tsjerk Wassenaar
Hi Stelios, Does your .trr file contain velocities? Cheers, Tsjerk On Sep 26, 2012 8:24 PM, Stelios Karozis skaro...@ipta.demokritos.gr wrote: Thanks for the response. First i tried the .trr from the simulation and the result was segmentation fault. I use g_covar for entropy estimation

[gmx-users] Intercalation DNA-Ethidium bromide

2012-09-27 Thread Hovakim Grabski
Dear Gromacs users, I've been running several simulations involving 26 base pairs B-DNA  and ethidium bromide. I used Autodock vina for finding inital binding sites and found one in the small groove. After that I ran a simulation of 14 ns. When I check the rmsd of Ethidium Bromide,there's a

Re: [gmx-users] pca-based MD

2012-09-27 Thread James Starlight
Dear all! I've read some reference papers about EDA sampling methods and found such usefull things. First of all as I understood for biassing MD simulation along several PCs extracted from another run the make_edi -radacc 1-3 option is exactly what I need. But I havent still understood about

Re: [gmx-users] Regarding RMSD analysis result

2012-09-27 Thread Tsjerk Wassenaar
Hi Ahmet, What exactly is the RMSD? Well, it's the average distance between corresponding particles in two structures. So, an RMSD of 2 nm means that, on average, each particle moved by 2 nm. How large is your protein at the start? How likely is it that you have such differences on average, after

Re: [gmx-users] rapid change in the angle of simulation cell - regd

2012-09-27 Thread Tsjerk Wassenaar
Hi Ramesh, Did you note how your atoms didn't change their positions? And how you can still stack them using either set of vectors? It's a great example of how PBC works. It's not the box that's important, not the vectors, but the infinite simulation system that results from stacking the unit

Re: [gmx-users] Do not want to add hydrogens to intial pdb structure

2012-09-27 Thread Peter C. Lai
Specify a united atom forcefield? You can also do a direct conversion from pdb to gro using editconf, but that's not going to generate a topology. On 2012-09-27 03:38:15PM +0530, mohan maruthi sena wrote: Hi all, When we generate .gro , .top files using pdb2gmx command it add

Re: [gmx-users] g_tcaf segmentation fault

2012-09-27 Thread Stelios Karozis
Hi Tsjerk, I checked my .trr file and it contains the velocities, as it should. Stelios On 09/27/2012 09:12 AM, Tsjerk Wassenaar wrote: Hi Stelios, Does your .trr file contain velocities? Cheers, Tsjerk On Sep 26, 2012 8:24 PM, Stelios Karozis skaro...@ipta.demokritos.gr wrote: Thanks for

Re: [gmx-users] g_tcaf segmentation fault

2012-09-27 Thread Stelios Karozis
Sorry, but i was wrong, the .trr file contains trajectories and the .gro output file contains velocities as it should. Stelios On 09/27/2012 03:03 PM, Stelios Karozis wrote: Hi Tsjerk, I checked my .trr file and it contains the velocities, as it should. Stelios On 09/27/2012 09:12 AM, Tsjerk

Re: [gmx-users] g_tcaf segmentation fault

2012-09-27 Thread Tsjerk Wassenaar
Hi Stelios, But the eigenvec.trr does not. You shouldn't be using that. So what exactly are you doing? How many frames do you have in your .trr file, what do you give for selections, etc? Please paste the exact commands and resulting output. Cheers, Tsjerk On Thu, Sep 27, 2012 at 2:03 PM,

Re: [gmx-users] g_tcaf segmentation fault

2012-09-27 Thread Tsjerk Wassenaar
The .trr file can contain coordinates, velocities, and forces over time, depending on your .mdp settings (nstxout, nstvout, nstfout). For g_tcaf, you need to have velocities. It does say so in the manpage. Run gmxcheck to see what's in your .trr file. A segmentation fault with the analysis tools

[gmx-users] tau_t and tc_grps for v-rescale

2012-09-27 Thread Felipe Pineda, PhD
Hi, I'd greatly appreciate any general advice on the possibility to use several (2 or more) tc_grps with v-rescale and how large could be tau_t with this coupling method (is 0.3 ps still OK?). Many thanks in advance and best regards, Felipe -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] distance restraint

2012-09-27 Thread Paula Andrea Delgado Pinzon
Hello gromacs users, I am doing energy minimization of a big protein with distance restraint (i need to create interactions between a group of residues, so i need them to be close), but in the resultant pdb a don't see those residues close, so how can I verify that the distance restraint are

[gmx-users] g_clustsize

2012-09-27 Thread mohammad agha
Dear Gromacs users I have one big problem with g_clustsize! I see 9 micelles in my system after running. When I use g_clustsize for number of clusters and average cluster size, they don't emphasize each other, and I see 9 micelles from 36 ps to 120 ps in my box, but results of

Re: [gmx-users] g_clustsize

2012-09-27 Thread Justin Lemkul
On 9/27/12 2:47 PM, mohammad agha wrote: Dear Gromacs users I have one big problem with g_clustsize! I see 9 micelles in my system after running. When I use g_clustsize for number of clusters and average cluster size, they don't emphasize each other, and I see 9 micelles from 36 ps to

Re: [gmx-users] distance restraint

2012-09-27 Thread Justin Lemkul
On 9/27/12 12:04 PM, Paula Andrea Delgado Pinzon wrote: Hello gromacs users, I am doing energy minimization of a big protein with distance restraint (i need to create interactions between a group of residues, so i need them to be close), but in the resultant pdb a don't see those residues

[gmx-users] Re: distance restraint

2012-09-27 Thread pauladelgado
*file alfadrest.itp* [ distance_restraints ] ; i j ? label funct loup1up2 weight 8002 10641 1 0 10.40.50.6 1 8040 10616 1 0 10.40.50.6 1 8067 10582 1 0