:
On 6/11/13 1:11 AM, mu xiaojia wrote:
Hi guys,
I am using simulated annealing for my protein+water+Ion system, I tried
to
let the system stay at some temperature for a while, e.g.: stay at 600k
from 3000ps to 1 ps, then gradually cool it down to 298k, so my mdp
is
like
Hi guys,
I am using simulated annealing for my protein+water+Ion system, I tried to
let the system stay at some temperature for a while, e.g.: stay at 600k
from 3000ps to 1 ps, then gradually cool it down to 298k, so my mdp is
like:
annealing_time = 0 3000 1 2 0 3000 1 2 0
Dear users,
I have used gromacs a while, however, sometime, when I run it on
supercomputer-clusters, I saw mdrun will generate a lot of files with #,
which occupied a lot of space, does anyone know why and how to avoid it?
Thanks
example, my commandmdrun_mpi -s -deffnm job -cpi -append
then
Dear GMX users,
I am not sure if someone has similar problems before. I cannot read half of
the frames from trr file after md simulation, and I believe my simulation
has already completed.
I have finished simulations A and B with both gmx4.5.4 and gmx4.5.5. the
only difference between A and B is
Sorry for the typo, the last evidence4) I also compared the generated
files' sizes, A = B in trr, edr , gro, cpt, if B crashes before reaching
100ns, the size would **NOT*** be the same as A.
On Wed, Apr 3, 2013 at 7:25 PM, mu xiaojia muxiaojia2...@gmail.com wrote:
Dear GMX users,
I am
Dear GMX users,
I have some trajectories of Ala-Ala dipepetides with COOH terminals
(Cap-Ala-Ala-COOH), However, I saw the chirality of the Ala-COOH doesn't
maintained as L form during the simulation, there are D-forms, is it
because there are some lacks of parameters of this part or Gromacs
probably means your trajectory is not continuous enough. I saw the same
thing when I try to fit an ensemble trajectory, which each frame is not
from the previous one. Or if your first frame in your trajectory is not
good looking(or having good rmsd to your target structure), fit option
cannot fit
try trjconv, maybe your reference gro/tpr file is cubic?
make sure:
trjconv -s the_dodecahedral_generated.tpr -f the_dodecahedral_generated.gro
-o your_aim.pdb
On Tue, May 22, 2012 at 9:27 AM, patrick wintrode pat_w...@yahoo.comwrote:
After generating my protein .gro and .top files and doing
(intermolecularly and
intramolecularly)
Thanks very much!
On Fri, May 18, 2012 at 7:57 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 5/18/12 7:22 PM, mu xiaojia wrote:
Hi gmx-users,
I have a question might be explained before but I cannot understand from
the
previous , how to calculation
try put -s before -deffnm
mdrun_mpi -s -deffnm file_name -multi 120 -replex 250 -cpi -append
On Sun, May 20, 2012 at 4:50 PM, Tomek Wlodarski
tomek.wlodar...@gmail.comwrote:
Hi Francesco,
Thanks!
However, it does not work with my case..
tomek
On Sun, May 20, 2012 at 1:47 PM, francesco
Hi gmx-users,
I have a question might be explained before but I cannot understand from
the previous , how to calculation the intermolecular h-bonds between two
molecules? I saw someone mentioned using a second tpr file, but how to do
it specifically? Thanks very much!
Ja
--
gmx-users mailing
, it
is necessary to -pbc mol first, otherwise the molecules might be
broken for calculating scripts like matlab.
good to know this, thanks!
On Wed, May 2, 2012 at 8:03 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 03/05/12, *mu xiaojia *muxiaojia2...@gmail.com wrote:
Dear gmx users,
I have
Dear gmx users,
I have a question about using the trjconv -pbc options before analyzing my
trajectory. It's stated by Justin's tutorial that:
use trjconv to account for any periodicity in the system. The protein will
diffuse through the unit cell, and may appear to jump across to the other
side
Thanks for the reply!
On Thu, Apr 26, 2012 at 3:28 AM, Teemu Murtola teemu.murt...@cbr.su.sewrote:
On Thu, Apr 26, 2012 at 04:19, mu xiaojia muxiaojia2...@gmail.com wrote:
e.g, I want to make an HN group of both H and N from my 2nd residue,
There are multiple ways to achieve what you want
Dear gmx users,
I may have a silly question, how to make a group of two atoms from the same
molecule?
e.g, I want to make an HN group of both H and N from my 2nd residue,
I know for single one, commands in *.dat file is like:
nameN = resnr 2 and name N;
nameH = resnr 2 and name H;
nameN;
Dear gmx-users,
I want to make a long nano-fiber composed of many non-covalently bonded
proteins, it elongates along the Z axial direction.
in editconf, we can define the Distance between the solute and the box,
but it works for x,y and z directions at the same time.
e.g. my command
editconf -f
Hi gmx-users,
It has been days that I cannot log into www.*gromacs*.org, does anyone know
anything happed to it?
Or is there any alternative website that we can see the documentation on
www.*gromacs*.org/Documentation/
Thanks very much!
Xiaojia
--
gmx-users mailing list
Dear GMX-users,
I found a question in 2009 asking which format of improper does
OPLS dihedral gromacs use. I have the same question, is it periodic or
harmonic?
If it is periodic, why in its ffbonded.itp file: #define improper_O_C_X_Y
180.0 43.93200 2 what do they mean?
Also, when I plug in
1 check with the rtp files in your forcefield, especially the parameters
2 check with the imput pdb file, the format matters a lot.
On Wed, Oct 19, 2011 at 8:18 AM, aiswarya.pa...@gmail.com wrote:
Hi Users,
I performed a simple minimization for a protein complex in vacuum. Didn't
get any
Dear gmx-users,
Does anyone know where can I find any explanations about the atom names in
ffbonded.itp file in oplsaa.ff? I am trying to compare the amino acids'
parameters in gromacs 4.5.4 with in tinker. Or where to find the default
parameters gromacs takes for amino acids in its
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