Mark,
I have written a new force field for my polymer. I have used this force
field for polymer in water. It worked fine. When I tried to put polymer
with nanotube in water, then I had this strange problem (My force field
worked fine for nanotube alone). Anyway I will try to rerun it.
Thank you f
Does it always do it at the same point/time?
To assist in tracking down what is happening, if the location is
reproducable, then get the trajectory to write out at much shorter
differences, so you can see what is actually happening as the time
approaches where things all go wrong and blow up.
Cat
> On Wed, 2006-07-05 at 15:11 +1000, Mark Abraham wrote:
>> > Mark,
>> >
>> > Thank you for your reply. When I checked step38885.pdb, I found a
>> > polymer chain in my system fall apart (bond broken). If I visualize
>> the
>> > trajectory. it is fine till step38000 (last frame in my trr file).
>>
On Wed, 2006-07-05 at 15:11 +1000, Mark Abraham wrote:
> > Mark,
> >
> > Thank you for your reply. When I checked step38885.pdb, I found a
> > polymer chain in my system fall apart (bond broken). If I visualize the
> > trajectory. it is fine till step38000 (last frame in my trr file).
>
> OK...
> Mark,
>
> Thank you for your reply. When I checked step38885.pdb, I found a
> polymer chain in my system fall apart (bond broken). If I visualize the
> trajectory. it is fine till step38000 (last frame in my trr file).
OK... bonds don't just "break" in MD simulations. Bonded potentials don't
all
Mark,
Thank you for your reply. When I checked step38885.pdb, I found a
polymer chain in my system fall apart (bond broken). If I visualize the
trajectory. it is fine till step38000 (last frame in my trr file).
I don't understand why the bond breaks after 76 ps simulation and why KE
doubles sudde
> Dear GMX users,
>
> After I edit vdwradii.dat and run genbox, my program still crashes when
> I run position restrained MD with heating the system from 100K to 300K.
> When I check the log file. I find the kinetic energy doubles (step 38880
> compare to step 38870, by the way, the re_t is the sam
Dear GMX users,
After I edit vdwradii.dat and run genbox, my program still crashes when
I run position restrained MD with heating the system from 100K to 300K.
When I check the log file. I find the kinetic energy doubles (step 38880
compare to step 38870, by the way, the re_t is the same in these
mark,
That is a good idea. Thank you very much!
Dongsheng
On Tue, 2006-07-04 at 15:38 +1000, Mark Abraham wrote:
> Dongsheng Zhang wrote:
> > Mark,
> >
> > Thank you for your reply. EM works fine before position-restrained MD.
> > Do you have any other suggestion besides to reduce the number
> position-restrained MD. Do you have any other suggestion
> besides to reduce the number of water inside the nanotube? Thanks!
Another option is to write a script that will do it for you
automatically.
Catch ya,
Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
V
Dongsheng Zhang wrote:
Mark,
Thank you for your reply. EM works fine before position-restrained MD.
Do you have any other suggestion besides to reduce the number of water
inside the nanotube? Thanks!
You could edit vdwradii.dat in the gromacs/share/top directory to give
either the water atoms
Mark,
Thank you for your reply. EM works fine before position-restrained MD.
Do you have any other suggestion besides to reduce the number of water
inside the nanotube? Thanks!
Dongsheng
On Tue, 2006-07-04 at 15:23 +1000, Mark Abraham wrote:
> Dongsheng Zhang wrote:
> > Dear GMX users,
> >
>
Dongsheng Zhang wrote:
Dear GMX users,
I am studying a system of a capped nanotube with a polymer in water.
When I use genbox, some water will be inside of the nanotube. This might
cause bad contact of water molecules inside of nanotube. Does anyone
know how to control the total number of water
Dear GMX users,
I am studying a system of a capped nanotube with a polymer in water.
When I use genbox, some water will be inside of the nanotube. This might
cause bad contact of water molecules inside of nanotube. Does anyone
know how to control the total number of water molecules inside the
nano
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