Dear all,
Could you please tell me, if this is normal during running a simulation. I
am running mdrun with -v flag and i receive this,
.
.
vol 0.23! imb F 2264% pme/F 0.57 step 1496300, will finish Mon Jan 21
00:13:42 2019
vol 0.23 imb F 3249% pme/F 0.75 step 1496400, will finish Mon Jan 21
00:13
Hi,
I have obtained a 100 ns simulation using Amber. I would like to calculate
the potential energy (VDW, COUL,ect) from the trajectory, below is my
command.
$gmx grompp -f test.mdp -p ../gromacs.top -n ../index.ndx -c ../300.pdb -o
rerun.tpr -maxwarn 1
$gmx mdrun -rerun ../protein.trr -s rerun.
Dear M,
Yup the timestep is enormous, but the Gromacs demo used 0.005 ns. At that
point the 2700 and the Ti started flinging waters molecules off into the ozone.
For the very short runs at 0.005 ~1400 ns/day was being hit. Usually the ts I
use is 0.002
Getting the ion and SOL concentration
On 11.01.2019 19:55, pbuscemi wrote:
> For those of you considering a workstation build and wonder about AMD
> processors I have the following results using the included npt and log intro
> for the villin headpiece in ~ 8000 atoms spc/e. The npt was run from a
> similar nvt ( 10 steps ) . Th
Dear Users,
For those of you considering a workstation build and wonder about AMD
processors I have the following results using the included npt and log intro
for the villin headpiece in ~ 8000 atoms spc/e. The npt was run from a similar
nvt ( 10 steps ) . The best results were achieved wi
On 1/11/19 8:12 AM, ZHANG Cheng wrote:
I got the a99SBdisp force field with a tip4pd.itp water model. How can I
convert it to a tip4pd.gro file?
I need this water gro file for "gmx solvate".
You can use the normal tip4p.gro that is provided already. After
minimization/equilibration, the
I got the a99SBdisp force field with a tip4pd.itp water model. How can I
convert it to a tip4pd.gro file?
I need this water gro file for "gmx solvate".
Thank you!
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Yes Mark!
"Can't read 1048576 bytes of 'traj.trr' to compute checksum. The file has been
replaced or its contents have been modified. Cannot do appending because of
this condition."
Thank you
Best
Rita
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
On Beh
Thank you Justin and Mark.
Using "-water select" works:
Select the Water Model:
1: TIP4P-D TIP 4-point with increased dispersion
2: None
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Fri, Jan 11, 2019 00:51 AM
To: "gromacs.org_gmx-users"
You can use plumed, as long as you are scaling all of your protein (as
you would be with REST2). You just need to post-process the output of
the plumed partial_tempering script:
https://groups.google.com/d/msg/plumed-users/lo-Sb8aUepY/X54UEB-tAgAJ
https://groups.google.com/d/msg/plumed-users/Tx
Hi,
If you want to append (because gmx mdrun -append is on by default), then
mdrun will check that your output files are unchanged. Either leave them
unchanged, or tell mdrun that you are not appending with gmx mdrun
-noappend. Does the error message that I presume you saw suggest the latter?
Mar
Dear all,
although it is not necessary to restart the simulation, we need to have the
trajectory file in the folder where the MD runs ?! Can we use a shorter
trajectory file?
Thank you!
Rita Melo.
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