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
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
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
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
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
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
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
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
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,
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
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
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
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
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
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
*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
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