Dear Chris,
Thank you for your message. I uploaded everything to the redmine. I will
let you know how the simulation with generated velocities went.
I asked the authors about any exemplary input that worked with tip5p and
oplsaa, but I did not get anything...
Best,
Grzegorz
On 2013-10-04 17:2
Dear Grzegorz:
>From a quick look at your .mdp, I also suggest that you go back to your system
>including the peptide that you had managed to finish EM with modified flexible
>tip5p but then crashed with the standard rigid tip5p during MD and try the MD
>again using gen-vel = yes
if you're sti
Dear Chris,
By now 7ns of the MD passed without a single warning.
Best Regards,
Grzegorz
P.s. The mdp:
constraints = none
integrator = md
dt = 0.001; ps
nsteps = 1000 ; total 10 ns
nstcomm = 1000
nstxout =
One a system passes EM and a couple of ps of MD, is it always stable
indefinitely? If not, then
something is wrong somewhere.
-- original message --
Dear Chris,
I put one tip5p molecule in a center of dodecahedral box - 2nm from that
molecule to walls, filled it with tip5p, ran 6000 steps of st
Dear Chris,
I put one tip5p molecule in a center of dodecahedral box - 2nm from that
molecule to walls, filled it with tip5p, ran 6000 steps of steep
minimization. After another 2704 steps of cg it converged to emtol 1.0.
I run 100k steps of nvt on this box afterwards
(http://shroom.ibb.waw.pl
Dear Chris,
I did not post the redmine issue yet, I want to check every possibility
beforehand. I will analyze trajectories more closely now.
Best,
Grzegorz
On 2013-09-29 18:47, Christopher Neale wrote:
Dear Grzegorz:
Under no conditions should any of the tip5p geometry change (for the
standa
Dear Grzegorz:
Under no conditions should any of the tip5p geometry change (for the standard
tip5p model).
If you find that this is happening, then that is certainly an error. You can
check if you like by analyzing
your trajectory. However, flexible bonds will allow the distance from the
argi
error
for the combination of oplsaa and tip5p.
Chris.
gigo gigo at ibb.waw.pl
Sun Sep 29 00:59:42 CEST 2013
Previous message: [gmx-users] OPLS/AA + TIP5P, anybody?
Next message: [gmx-users] Restarting simulation -s. files?
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
Dear Chris,
s point it is a good idea for you to file a redmine issue. It's
not a gromacs error per se, but
if this is true then pdb2gmx or grompp should give a warning or error for the
combination of oplsaa and tip5p.
Chris.
gigo gigo at ibb.waw.pl
Sun Sep 29 00:59:42 CEST 2013
Previous message:
Dear Chris,
I am really grateful for your help. This is what I did, with additional
LJ terms on LP1 and LP2 of tip5p:
- 5000 steps of steepest descent with positions restraints on protein
and flexible water (flexibility like in tip4p),
- 5000 steps of steep, no restraints, flexible water,
- 500
Dear Gigo:
everything that I suggested was just ways that you might get a system without
bad contacts to
start your simulation with the proper (standard) tip5p model and oplsaa. I
expected that combination
to work together since they came out of the same lab, but looking at the
initial tip5p pa
Dear Chris,
Thank you for your reply. I defined a new virtual atomtype (type D) with
LJ sigma 1.72A ( 2*0.7+1.72=3.12, which is sigma of the oxygen) and
played a bit with epsilon till the new LJ repulsion was able to prevent
the build up of a huge force on the oxygen while interacting with
dim
Dear Gigo:
I've never used tip5p, but perhaps you could add some LJ terms to the opls_120
definition,
do your minimization, then remove the fake LJ term on opls_120 and run your MD?
If that doesn't work, then you might be able to minimize your system using
FLEXIBLE tip3p
water and then use a sc
Dear Mark,
Thank you for your reply. Unfortunately, TIP5P is completely rigid and
the FLEXIBLE define will not change it. Any other ideas?
Best,
g
On 2013-09-24 23:51, Mark Abraham wrote:
You should be able to minimize with CG and TIP5P by eliminating
constraints, by making the water use a fle
You should be able to minimize with CG and TIP5P by eliminating
constraints, by making the water use a flexible molecule, e.g. define
= -DFLEXIBLE (or something). Check your water .itp file for how to do
it.
Mark
On Tue, Sep 24, 2013 at 10:25 PM, gigo wrote:
> Dear GMXers,
> Since I am intereste
Dear GMXers,
Since I am interested in interactions of lone electron pairs of water
oxygen within the active site of an enzyme that I work on, I decided to
give TIP5P a shot. I use OPLSAA. I run into troubles very fast trying to
minimize freshly solvated system. I found on the gmx-users
(http:/
16 matches
Mail list logo
