On 10/16/12 7:42 AM, ahmet yıldırım wrote:
Hi,
I converted a .tpr file to .pdb using editconf.
editconf -f md.tpr -o new-md.pdb
I visualised new-topol.pdb using pymol. It has the virtual sites.
Furthermore, the molecule(s) does not stay in the centre of the box.
I need a proper .tpr or .pdb fi
Hi,
I converted a .tpr file to .pdb using editconf.
editconf -f md.tpr -o new-md.pdb
I visualised new-topol.pdb using pymol. It has the virtual sites.
Furthermore, the molecule(s) does not stay in the centre of the box.
I need a proper .tpr or .pdb file for analysis.
How can these problems fixed?
ana johari wrote:
Dear user,
During simulation I restart the Md run and know I have two .tpr file.
Because my molecule split over boundary after 1 ns of simulation,I want
to use “trjconv” as a command to center my molecule but I don’t know to
chose my first tpr file( for the first 1ns) or t
Dear user,
During simulation I restart the Md run and know I have two .tpr file. Because
my
molecule split over boundary after 1 ns of simulation,I want to use “trjconv”
as
a command to center my molecule but I don’t know to chose my first tpr file(
for
the first 1ns) or the second one after
- Original Message -
From: Carla Jamous
Date: Tuesday, May 25, 2010 22:54
Subject: [gmx-users] tpr file
To: Discussion list for GROMACS users
> Hi everyone,
>
>
> please I have an important question:
> When I continue my simulation, I do: tpbconv -s .tpr -ex
Carla Jamous wrote:
Hi everyone,
please I have an important question:
When I continue my simulation, I do: tpbconv -s .tpr -extend-s .tpr
mdrun -v -s
.tpr -cpi .cpt -cpo .cpt -o .trr -c .gro -x .xtc -e .edr -g .log
At one poin
Hi everyone,
please I have an important question:
When I continue my simulation, I do: tpbconv -s .tpr -extend-s .tpr
mdrun -v -s .tpr
-cpi .cpt -cpo .cpt -o .trr -c .gro -x .xtc -e .edr -g .log
At one point of my simulation, I had
> Dear GMX users,
>
> The following message is from a tpr file by gmxdump command:
>
> atom[ ]={type= 4, typeB= 4, ptype=Atom, m= 1.20110e+01,
> q=-5.29400e-01, mB= 1.20110e+01, qB=-5.29400e-01, resnr= 32}
> grpnrs=[ 0 0 0 0 0 0 0 0 0 0 ]}
>
> Could anyone tell me what does "type= 4"
Dear GMX users,
The following message is from a tpr file by gmxdump command:
atom[ ]={type= 4, typeB= 4, ptype=Atom, m= 1.20110e+01,
q=-5.29400e-01, mB= 1.20110e+01, qB=-5.29400e-01, resnr= 32}
grpnrs=[ 0 0 0 0 0 0 0 0 0 0 ]}
Could anyone tell me what does "type= 4" mean? I have ch
Dhananjay wrote:
Hello all,
Using trjcat I have joined 3 *.trr files and got final *.trr file.
How to get/genetare corresponding *.tpr file ?
According to manual, the tpr file extension stands for portable binary
run input file. This file contains the starting structure of your
simulation,
Hi Dhananjay,Basically, you can choose whichever tpr file you like. If you just want to have the information about bonds, angles, etc, it's all the same. However, if you want to relate your frames to a given reference (
e.g. for calculating the RMSD), it will matter. Which one you'll have to choose
Hello all,
Using trjcat I have joined 3 *.trr files and got final *.trr file.
How to get/genetare corresponding *.tpr file ?
According to manual, the tpr file extension stands for portable binary run input file. This file
contains the starting structure of your simulation, the molecular topo
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