Please don't double post. We saw the first one.
1. That is a question with a lot of options. Do you want a grid of
proteins? then try genbox -cp empty_big.gro -cs one_protein.gro
2. What do you mean by remove pbc? Try trjconv -pbc mol -ur compact to
get an "enforced" pbc, or starting from
Dear Dr. Warren:
Thank you for your answer and sorry for my ignorantness.
I will do more literature survey...
Thank you again.
Sincerely,
Kim
On Sun, Mar 22, 2009 at 11:30 PM, Dallas B. Warren <
dallas.war...@pharm.monash.edu.au> wrote:
> Kim,
>
> >Recently I have been focusing on cross-lin
On Mon, Mar 23, 2009 at 10:31 AM, wrote:
> Hello everyone,
>
>
> There is following warning given in the GROMACS home page,
>
>
> WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These
> compilers come with recent Linux distrubutions like Fedora 5/6 etc.
>
Hello everyone,
There is following warning given in the GROMACS home page,
WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These
compilers come with recent Linux distrubutions like Fedora 5/6 etc.
Can anyone please tell me that whet
Hello Justin Sir,
Greetings from Pawan.
Sorry for the late reply.
The max. force was 1.2447973e+o5 on atom 19448.
This particular atom belongs to one of the lipid residues of the bilayer.
I get Lincs warnings whenever I run the position restraint mdrun.
Thanking you,
Pawan
On Sat, Mar 21, 2009
Kim,
>Recently I have been focusing on cross-linking phenomenon of polymers.
>As far as I understood, cross-linking include bond breaks in one
polymer chain and bond occurrences among broken chains.
>I guess OPLS-aa is not suitable for this purpose, and my question is
this.
>Is my guess correct?
Dear All:
I appreciate your care and help all the time.
As you may know I am trying to simulate polymer behaviors.
Recently I have been focusing on cross-linking phenomenon of polymers.
As far as I understood, cross-linking include bond breaks in one polymer
chain and bond occurrences among broke
Hello,
I have been trying to figure out why I'm getting this message. I
looked over this site
http://chemistry.csulb.edu/ffamber/index.html#usage
But could not figure out why I'm getting this error. I'm running
pdb2gmx_d.exe -ff amber03
WARNING: atom H is missing in residue LYSH 124 in the pdb
Hi, All:
I have three questions:
(1) How can I add more than one protein into a cell with PBC, maybe 10
proteins? How can I modify the command of editconf and genbox to achieve the
above function?
(2) How to remove the PBC of the cell? I use the option '-pbc no' in the
editconf fiat, but it can
Hi, All!!
I have four questions:
(1) How can I add more than one protein into a cell with PBC, maybe 10
proteins? How can I modify the command of editconf and genbox to achieve the
above function?
(2) How to remove the PBC of the cell? I use the option '-pbc no' in the
editconf fiat, but it can
Hi, have you set comm-mode = None? If no, you can set it and try again.
Zhongqiao Hu
Dept of Chemical and Biomolecular Engineering
National University of Singpore
>Hello,
>I want to simulate a rigid plate (wall) moving along one direction and
>reflecting all the particles it meets
Hi,
do you get any other error messages? (Check md.log and the output)
You might want to use 4.0.4 instead of 4.0.2. (Some bugs have been fixed)
Roland
2009/3/22 KS Rotondi :
> Dearest All,
>
> I'm experiencing strange behavior running Gromacs 4.0.2 on dual G5
> macintoshs (OS 10.4.11) in my co
Dearest All,
I'm experiencing strange behavior running Gromacs 4.0.2 on dual G5
macintoshs (OS 10.4.11) in my college's computer laboratory. When I
use the attached .mdp file, grompp ends in a seg fault, however if I
remove the last 3 lines (controlling velocity generation) grompp runs
n
Zhong Zheng wrote:
Dear all
I have successfully run though the energy minimization on my target
protein. I am trying to extract the backbone-backbone interactions from
the energy output files. My understanding is that I need to define the
energy groups in the grompp.mdp. This is what I edit
Dear all
I have successfully run though the energy minimization on my target
protein. I am trying to extract the backbone-backbone interactions
from the energy output files. My understanding is that I need to
define the energy groups in the grompp.mdp. This is what I edited:
energygrps
Hi,
1)
The "compressibility" or elastic tensor is a full tensor.
You only mention the three eigenvectors and eigenvalues,
but there are off-diagonal components.
I would assume all the eigenvalues are very close.
As a rough guess I would just use the same value for all diagonal
and off-diagonal co
varsha gautham wrote:
Dear gmx user,
Am a beginner to gromacs,I have a few questions to be clarified before
getting started with gromacs.
You probably want to start by reading a textbook (or the gromacs manual)
and some review papers.
1.on giving pdb2gmx gromacs offers force fields fom
Varsha: have you subscribed to the list yet? Please do so if you
haven't.
On Sun, 2009-03-22 at 13:18 +0400, varsha gautham wrote:
> 3. hen how to choose a timestep for a simulation like a picosecond or
> a nanosecond?What is a timestep?
>
> I have gone through many materials and stuffs related t
On Sun, Mar 22, 2009 at 2:52 PM, varsha gautham
wrote:
> Dear gmx user,
>
>
> Am a beginner to gromacs,I have a few questions to be clarified before
> getting started with gromacs.
>
> 1.on giving pdb2gmx gromacs offers force fields fom 0 to 6 and also i
> read like opls-aa is the best forcefield
Dear gmx user,
Am a beginner to gromacs,I have a few questions to be clarified before
getting started with gromacs.
1.on giving pdb2gmx gromacs offers force fields fom 0 to 6 and also i
read like opls-aa is the best forcefield for protein? why is that
so?What kind of forcefield do i have to choo
Dear gmx user,
Am a beginner to gromacs,I have a few questions to be clarified before
getting started with gromacs.
1.on giving pdb2gmx gromacs offers force fields fom 0 to 6 and also i
read like opls-aa is the best forcefield for protein? why is that
so?What kind of forcefield do i have to choo
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