On Aug 30, 2014 12:32 PM, "Alberto Sergio Garay"
wrote:
>
> Hi all
>
> I'd like to count the number of bonding and non-bonding interactions in a
one molecule system in vacuo, just for educational purpose. Is there any
way to obtain that info in Gromacs..?
Hi,
Not really - it depends on the force
On 8/31/14, 1:55 PM, Alex s wrote:
There was a typo in the last message, I found NO issues in point 2.
Actually, you did. You said when you removed the ions, the problem was
resolved. That indicates to me that the ions are somehow unstable. I don't
know much about doing CG simulations,
There was a typo in the last message, I found NO issues in point 2.
From: as1...@hotmail.com
To: gmx-us...@gromacs.org
Date: Sun, 31 Aug 2014 18:52:39 +0100
Subject: Re: [gmx-users] Segmentation fault mdrun
Thanks for the reply
I've attached a copy of my mdp file. It is a coarse grained system so
Thanks for the reply
I've attached a copy of my mdp file. It is a coarse grained system so a time
step of 0.04 shouldn't be a problem. Regarding the link you've given, points 1
and 4 are not applicable to my situation, I've tried point 2 and found issues.
What should I be looking for in point 3?
On 8/31/14, 1:17 PM, Alex s wrote:
Hi
I'd really appreciate some advice on this issue, I tend to get a segmentation
fault during my mdrun. I've searched online for ways to resolve this and tried
to diagnose whats causing this problem but I'm having no luck.
I know that if you get a segmentati
Hi
I'd really appreciate some advice on this issue, I tend to get a segmentation
fault during my mdrun. I've searched online for ways to resolve this and tried
to diagnose whats causing this problem but I'm having no luck.
I know that if you get a segmentation fault at step 0 its most likely a
2014-08-31 16:29 GMT+01:00 Justin Lemkul :
> examining the contents of the file, and also by noticing there are
> probably a ton more data points than there are residues, so it can't be
> averages.
So I did and so I tought. I just wanted to make sure. Thank you :).
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Gromacs Users mailing lis
On 8/31/14, 11:27 AM, Dawid das wrote:
Dear Gromacs experts,
I am wondering what I actually see when I plot output from g_rama. When I
run it like this:
g_rama -f 3ldj-npt-md.trr -s npt-md.tpr -o 3ldj-npt-rama.xvg
I plot the output using:
xmgrace 3ldj-npt-rama.xvg
Now I see Ramachandran pl
Dear Gromacs experts,
I am wondering what I actually see when I plot output from g_rama. When I
run it like this:
g_rama -f 3ldj-npt-md.trr -s npt-md.tpr -o 3ldj-npt-rama.xvg
I plot the output using:
xmgrace 3ldj-npt-rama.xvg
Now I see Ramachandran plots with squares and phi and psi angles on
Hi,
I assumed that you had gone through the forcefield.ff files on Slipids
webpage. You need to include the following section at the end in your
ffnonbonded.itp (some of the spaces may be missing below). I suggest
modifying a local copy of your desired Amber ff.
; SLIPIDS STARTS HERE
HAL11
On 8/31/14, 8:42 AM, Yorquant Wang wrote:
Hi,
I have done that according to your advice and when I do the command
grompp, I get such a error:
Fatal error:
Atomtype NTL not found
-
this is my top file:
#include "amber99sb-ildn.ff/forcefield.itp"
#include "POPC.itp"
#inc
On 8/31/14, 8:20 AM, rajat desikan wrote:
Hi,
Slipids are already compatible with Amber. Just download the proper
lipid.itp file (DPPC.itp, DMPC.itp, ...) from the Slipids website, and
include the below line in your .top after processing your protein with
pdb2gmx (and selecting some Amber FF).
On 8/31/14, 6:59 AM, Yorquant Wang wrote:
Hi all,
I want to do a membrane protein simulation and I want to use amber FF
for protein (my target protein contains many beta sheet secondary
structures). But forcefield.ff file in the web:
http://people.su.se/~jjm/Stockholm_Lipids/Downloads.h
On 8/31/14, 6:51 AM, Dawid das wrote:
Dear Gromacs experts,
Is there a tool in Gromacs which allows one to calculate mean length,RMSD,
the minimum and maximum length of a specific bond? If yes, is it possible
to calculate it only for a specific time period of MD simulation, e.g. 3-5
ns?
g_b
On 8/30/14, 8:09 AM, Mana Ib wrote:
Thankyou for your response. I spaced them at approx 0.05nm because at the
473rd configuration my ligand becomes solvated...and completely dissociated
from the protein and there is a jump in the COM distances. Would you
recommend running windows for configurat
On 8/30/14, 7:17 AM, Negar Parvizi wrote:
Dear Gromacs users
I have submitted a simulation for 10 ns. Now when I started to plot the graphs
such as RMSD, I saw that it has stopped at 8 ns. The point is that although the
run has stopped before specified time, I see in md.log file the time repo
Hi,
I have done that according to your advice and when I do the command
grompp, I get such a error:
Fatal error:
Atomtype NTL not found
-
this is my top file:
#include "amber99sb-ildn.ff/forcefield.itp"
#include "POPC.itp"
#include "protein-amber.itp"
#include "amber99sb-il
Hi,
Slipids are already compatible with Amber. Just download the proper
lipid.itp file (DPPC.itp, DMPC.itp, ...) from the Slipids website, and
include the below line in your .top after processing your protein with
pdb2gmx (and selecting some Amber FF).
; Include lipid topology
#include "./DMPC.it
Hi all,
I want to do a membrane protein simulation and I want to use amber FF
for protein (my target protein contains many beta sheet secondary
structures). But forcefield.ff file in the web:
http://people.su.se/~jjm/Stockholm_Lipids/Downloads.html, contains only
lipids parameter. I don't kn
Dear Gromacs experts,
Is there a tool in Gromacs which allows one to calculate mean length,RMSD,
the minimum and maximum length of a specific bond? If yes, is it possible
to calculate it only for a specific time period of MD simulation, e.g. 3-5
ns?
Best wishes,
Dawid Grabarek
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