Adam Fraser wrote:
Hello,
I'm trying to get started working with a system of 2 hexadecane
molecules in water but I'm having some trouble.
I'm getting the following error when I run:
grompp -f simulate.mdp -c 2Hex_solv.gro -p 2Hex.top -o md.tpr
Program grompp, VERSION 3.3.2
Source code file
Hello,
I'm trying to get started working with a system of 2 hexadecane molecules in
water but I'm having some trouble.
I'm getting the following error when I run:
grompp -f simulate.mdp -c 2Hex_solv.gro -p 2Hex.top -o md.tpr
Program grompp, VERSION 3.3.2
Source code file: readir.c, line: 794
Stéphane Téletchéa wrote:
David van der Spoel a écrit :
Stéphane Téletchéa wrote:
I've found out where the problem lie (at least one of ...).
Small reminder: i've tried to setup a system consisting of HIV
protease + one ligand on a water box. I used the excellent protocol
from John E. Kerrig
David van der Spoel a écrit :
Stéphane Téletchéa wrote:
I've found out where the problem lie (at least one of ...).
Small reminder: i've tried to setup a system consisting of HIV
protease + one ligand on a water box. I used the excellent protocol
from John E. Kerrigan (Drug-enzyme tutorial) i
Stéphane Téletchéa wrote:
I've found out where the problem lie (at least one of ...).
Small reminder: i've tried to setup a system consisting of HIV protease
+ one ligand on a water box. I used the excellent protocol from John E.
Kerrigan (Drug-enzyme tutorial) in order to set up my simulation
I've found out where the problem lie (at least one of ...).
Small reminder: i've tried to setup a system consisting of HIV protease
+ one ligand on a water box. I used the excellent protocol from John E.
Kerrigan (Drug-enzyme tutorial) in order to set up my simulation and
encountered some prob
Hmm, yes, I do see your point. It was intended as a pun in reply to
Stephanes comment to my request for a lot of information. But I do
apologize in case people take offence. Maybe I should refrain from
answering under fatigue...
Tsjerk
On 5/25/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
>
If you could now send post your shoe size, your length and weight, and
pictures of worthwhile sisters if you have any, we might be able to
reinforce the incentive to help you :p
These comments are totally unacceptable. I suppose it started out as a
joke but it progresses into objectification o
Hi Stephane,
If you could now send post your shoe size, your length and weight, and
pictures of worthwhile sisters if you have any, we might be able to
reinforce the incentive to help you :p
I didn't imply you were a beginner (other maybe than a beginner with
Gromacs, as you indicate yourself).
Hi,
On May 24, 2007, at 10:06 AM, [EMAIL PROTECTED] wrote:
My amber experience is probably not good for gromacs since the
logic of using
files is sometimes different (and it seems heating, equilibration and
production is not used often in gromacs, probably due to the fact
you can
isolate
Selon Tsjerk Wassenaar <[EMAIL PROTECTED]>:
> Hi Stephane,
>
> I think this ends up in treating symptoms. Setting up a simulation of
> HIVP should not give such problems. It's probably best to start all
> over: pdb2gmx, EM in vacuum, editconf -d 1.0, genbox, EM in solvent,
> etc... Keep track of e
Hi Stephane,
I think this ends up in treating symptoms. Setting up a simulation of
HIVP should not give such problems. It's probably best to start all
over: pdb2gmx, EM in vacuum, editconf -d 1.0, genbox, EM in solvent,
etc... Keep track of everything you're doing, give all files an
informative n
Stéphane Téletchéa wrote:
Mark Abraham a écrit :
Stéphane Téletchéa wrote:
While switching from NVT to NPT, i'm crashing my simulation.
The error message seen is (repeated 10 times, then mdrun aborts):
#
Step 1 Warning: pressure scaling more than 1%, mu: -1.59647e+20
-1.59647e+20 -1.5964
Mark Abraham a écrit :
Stéphane Téletchéa wrote:
While switching from NVT to NPT, i'm crashing my simulation.
The error message seen is (repeated 10 times, then mdrun aborts):
#
Step 1 Warning: pressure scaling more than 1%, mu: -1.59647e+20
-1.59647e+20 -1.59647e+20
Correcting invalid b
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