[EMAIL PROTECTED] wrote:
Message: 1
Date: Tue, 26 Aug 2008 15:38:56 +0530 (IST)
From: [EMAIL PROTECTED]
Subject: [gmx-users] g_hbond output analysis
To: gmx-users@gromacs.org
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain;charset=iso-8859-1
hi
i used the -num option for g_hbond run. s
hi all
i can able to get .trr file after running md for 10 hrs
but i cannot able to get the .trr to .xtc file which gives out the
following error. can anyone guess, what type of error is this, & how to
resolve it..
Parthiban & Sundar
--- time
Dear justin
I cannot find my error.I make mix solvent tfe and spc ( was
minimized)and solvate on a peptide.I use ffg53a5 .I take this error
.I saw in line 61 in top file but there is not Ho in top file and
rtp file ffg53a5. what do i de?please help me.
Back Off! I just backed up mdout.mdp to .
Hi There,
I am running gromacs in a parellel architecture using -np 20.
Now I want to generate the energy plot using g_energy, but there are 20 .edr
files.
How should I use the g_energy command or which .edr file I should use?
Any suggestion would be of great help..
With Thanks,
Vivek
___
> Message: 1
> Date: Tue, 26 Aug 2008 15:38:56 +0530 (IST)
> From: [EMAIL PROTECTED]
> Subject: [gmx-users] g_hbond output analysis
> To: gmx-users@gromacs.org
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain;charset=iso-8859-1
>
> hi
>
> i used the -num option for g_hbond run. since i
Matt Wyczalkowski wrote:
I have a corrupt TRR file with a bad frame in the middle; I am
wondering if I can remove just the bad frame to utilize all of my good
data.
To obtain the corrupt TRR file, I first ran a simulation which died
(at about 37.9ns) due to a disk quota restriction; this first
I have a corrupt TRR file with a bad frame in the middle; I am
wondering if I can remove just the bad frame to utilize all of my good
data.
To obtain the corrupt TRR file, I first ran a simulation which died
(at about 37.9ns) due to a disk quota restriction; this first
simulation produced part1.tr
Chih-Ying Lin wrote:
Hi
the molecular structure : bond length, bond angle, dihedral angle
the bond length, bond angle are easily determined..
but the dihedral angle are hard to control...
Are you looking to control (i.e., restrain/constrain) these parameters, or
measure them?
with
Hi
the molecular structure : bond length, bond angle, dihedral angle
the bond length, bond angle are easily determined..
but the dihedral angle are hard to control...
with one set of the force field parameter, I could not get the exact
structure of the molecule (not all of the dihedral ang
In addition to that information, what parameters are you using for O2? It
sounds like something is super attractive within your system, causing the O2 to
condense. At what temperature are you simulating?
-Justin
Vitaly Chaban wrote:
Could you provide a movie or at least snapshots? What abo
Could you provide a movie or at least snapshots? What about energy of the system? How it changes?
>
Sorry I am not very good at describing my system. After running the simulation for a while or equilibrating the system all the oxygen molecules move along one wall (a rectangular box wi
[EMAIL PROTECTED] wrote:
Hi
I am doing a 5 peptide simulation in a 6nm box. Now to check the
correctness of my simulation i m calculating the minimum periodic distance
using g_mindist to find out the distance between molecule and its periodic
images.Following is the command i have used
g_mind
Hi
I am doing a 5 peptide simulation in a 6nm box. Now to check the
correctness of my simulation i m calculating the minimum periodic distance
using g_mindist to find out the distance between molecule and its periodic
images.Following is the command i have used
g_mindist -s full.tpr -f full.xtc -
Hi,
On Tuesday, 26. August 2008, Bhanu wrote:
> Hi,
> I'm using Gromacs 3.3.3, installed with double precision. When I run genion
> with this command:
>
> genion_d -s *.tpr -o *.gro -g genion.log -pot pot.pdb -p *.top -neutral
>
> the following error message was generated:
> --
Bhanu wrote:
Hi,
I'm using Gromacs 3.3.3, installed with double precision. When I run
genion with this command:
genion_d -s *.tpr -o *.gro -g genion.log -pot pot.pdb -p *.top -neutral
the following error message was generated:
--
Hi,
I'm using Gromacs 3.3.3, installed with double precision. When I run genion
with this command:
genion_d -s *.tpr -o *.gro -g genion.log -pot pot.pdb -p *.top -neutral
the following error message was generated:
Program g
Hi all!
>From an/during an MD simulation of a protein in water or urea solvent I
would like to extract the forces acting on certain protein atoms from the
whole solvent (that is, one protein atom but all solvent) at for example
every 10th timestep.
With nstfout I can set the frequency for o
Dear gmx-users,
does anybody know some references for C_v(heat cap) and viscosity values for
SPCE and the flexible version of SPC water ?
For SPC(rigid) , tip4p etc. are lot of literature references but I was not
able to find C_v and viscosity for the above mentioned cases...
Thank you for
> Using the parameters listed earlier I equalized my system after trying to
> place the oxygen and nitrogen molecules evenly throughout my system. The
> result showed the nitrogen molecules fairly even throughout the system but
> all the oxygen molecules on one side. Any ideas on why the system m
Hi,
On Tuesday, 26. August 2008, [EMAIL PROTECTED] wrote:
> hi
>
> i used the -num option for g_hbond run. since i new to gromacs i cannot
> able to interpret the output form. it comes in 3 columns with the first
> column indicating the frame, i dont know about the remaining two columns
if you us
hi
i used the -num option for g_hbond run. since i new to gromacs i cannot
able to interpret the output form. it comes in 3 columns with the first
column indicating the frame, i dont know about the remaining two columns
Kindly suggest
Parthiban & sundar
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