Hello
Please see my response below.
On Thu, Aug 11, 2011 at 10:23 AM, Mark Abraham wrote:
> On 11/08/2011 10:22 PM, Da-Wei Li wrote:
>
> Dear Mark and others
>
> I did more tests and thought that it might come from numerical error. The
> reasons are
>
> 1. If I use .trr file instead of the low
On 11/08/2011 10:22 PM, Da-Wei Li wrote:
Dear Mark and others
I did more tests and thought that it might come from numerical error.
The reasons are
1. If I use .trr file instead of the low precision xtc file, things
become better, ie, I get much less snapshots that has high energy.
That do
Dear Justin
You are right about the cut-off. The vdw energy spike disappeared after I
increased the cut-off in the rerun. But I still don't understand why? Can
the cutoff error build up to several thousand kj/mol for 100AA protein.
Again I would like to emphasize NOT to use a xtc file in MM/PBSA
Da-Wei Li wrote:
Dear Justin
An implicit water simulaiton with this short cutoff is problematic but I
think it is fine for rerun. I want to exactly repeat the original
energies in the explicit water MD.
The manu say "neighbor list searching will be performed for every frame"
with rerun op
Dear Justin
An implicit water simulaiton with this short cutoff is problematic but I
think it is fine for rerun. I want to exactly repeat the original energies
in the explicit water MD.
The manu say "neighbor list searching will be performed for every frame"
with rerun option. So that I don't thi
Da-Wei Li wrote:
Dear Mark and others
I did more tests and thought that it might come from numerical error.
The reasons are
1. If I use .trr file instead of the low precision xtc file, things
become better, ie, I get much less snapshots that has high energy.
2. I supplied -pforce in my m
Dear Mark and others
I did more tests and thought that it might come from numerical error. The
reasons are
1. If I use .trr file instead of the low precision xtc file, things become
better, ie, I get much less snapshots that has high energy.
2. I supplied -pforce in my mdrun -rerun and found tha
On 11/08/2011 1:45 AM, Da-Wei Li wrote:
Dear Mark
Could you please help me out? I can send you the trajectory (1000
snapshot in pdb format), mdp, topol file. I use Gromacs-4.5.3.
Not unless you can show me a shell script and .mdp file that can take
your original trajectory, do my suggested p
Dear Mark
Could you please help me out? I can send you the trajectory (1000 snapshot
in pdb format), mdp, topol file. I use Gromacs-4.5.3.
I checked the pdb file in UCSF Chimera and didn't find any crash. I have
about 10 snapshot that has high vdw energy.
best,
dawei
On Wed, Aug 10, 2011 at
On 11/08/2011 1:18 AM, Da-Wei Li wrote:
Dear Mark
That is my thought too.To test this possibility, I created a mdp file
without PBC and use trjconv -pbc nojump to make whole protein. >From
visualization in UCSF Chimera, the trajectory looks fine. But I still
have some snapshot that have very
Dear Mark
That is my thought too.To test this possibility, I created a mdp file
without PBC and use trjconv -pbc nojump to make whole protein. From
visualization in UCSF Chimera, the trajectory looks fine. But I still have
some snapshot that have very high vdw energy.
best
dawei
On Wed, Aug 10,
On 11/08/2011 12:29 AM, Da-Wei Li wrote:
Dear Gromacs users:
I recently tried some MM/PBSA stuff using the rerun function of mdrun
and GBSA model. All water molecules are stripped off the trajectory file.
However, when I examine the different energy term, it is disturbing
that short range vd
Dear Gromacs users:
I recently tried some MM/PBSA stuff using the rerun function of mdrun and
GBSA model. All water molecules are stripped off the trajectory file.
However, when I examine the different energy term, it is disturbing that
short range vdw energy of some snapshot are very high (> 100
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