Hi,
visualize your MD trajectory in VMD without water (or solvent) and without
ions (if have).
I hope this helps.
Regards,
Javier
2012/10/6 Albert
> hello:
>
> I am using the following command for md production in gromacs:
>
> grompp -f md.mdp -p md.top -o md.tpr
>
> mpirun -np 64 mdrun -s
it is because when i put
genbox -cp protein_box.gro -ci solvent.gro -nmol 1381 -p control.top
-o prot_solv.gro
the error turn out like this :
System total charge: 0.000
Grid: 17 x 16 x 14 cells
nri = 12718, nrj = 100152
Try 9119box_margin = 0.45overlap:
Killed
thats why i need to run genbox twi
Dear gmxers,
Sorry to all that pays attention to my previous post. When I looked into the
generated mdp files, I find that except the ele. potentials there is another
difference in the running parameters, namely cut-off. Now I am sure that it
is different cut-off that causes that big difference in
On 10/7/12 9:17 PM, shika wrote:
Thanks Justin.
May I ask something, if i'm using the command for genbox before
minimization which is
genbox -cp protein_box.gro -cs solvent.gro -p control.top -o prot_solv.gro
next i insert water by using same command;
genbox -cp prot_solv.gro -p control.top
On 10/7/12 12:13 PM, Andrew DeYoung wrote:
Hi,
My system is in the slab geometry; I have applied periodic boundary
conditions along x and y, but none along z.
I frequently use the handy tool g_potential (using the -oc switch) to
compute the (average) charge density (i.e., charge distribution
On 10/7/12 2:15 PM, Ladasky wrote:
Justin Lemkul wrote
Random segmentation faults are really hard to debug. Can you resume the
run
using a checkpoint file? That would suggest maybe an MPI problem or
something
else external to Gromacs. Without a reproducible system and a debugging
backtrace,
On 10/7/12 3:52 PM, Ali Alizadeh wrote:
Dear All users
How to can i replace a molecule(for example methane) with another
molecule(propane)?
Number of these molecules are given and their position is random,
Can I use genbox or genion, How to do i do it?
Likely you can't, as you were already
On 10/7/12 8:42 PM, Nur Syafiqah Abdul Ghani wrote:
Dear All,
Fatal error:
number of coordinates in coordinate file (prot_wtr_solv.gro, 18031)
does not match topology (control.top, 16650)
It happen when i started to minimize it by using the command
grompp -v -f minim_first.mdp
Dear All users
How to can i replace a molecule(for example methane) with another
molecule(propane)?
Number of these molecules are given and their position is random,
Can I use genbox or genion, How to do i do it?
Sincerely
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.
Justin Lemkul wrote
> Random segmentation faults are really hard to debug. Can you resume the
> run
> using a checkpoint file? That would suggest maybe an MPI problem or
> something
> else external to Gromacs. Without a reproducible system and a debugging
> backtrace, it's going to be hard to
Hi,
My system is in the slab geometry; I have applied periodic boundary
conditions along x and y, but none along z.
I frequently use the handy tool g_potential (using the -oc switch) to
compute the (average) charge density (i.e., charge distribution or a
"histogram of charges") along z for a part
On 10/7/12 12:24 AM, vidhya sankar wrote:
Dear justin Thank you for your previous reply
I am
running NPT Equlibration at 20 ps with dt 0.0002 in 10 steps Without
usage of Lincs Algorithm and its related paramete
12 matches
Mail list logo
