Alternatively, has anyone else reproduced the viscosity calculation, or
tried to?
If anyone would be so kind as to forward their input files, that might help
me narrow down the problem with my own input files.
Thank you.
James
On 11 April 2013 16:55, James Cannon jamesresearch...@gmail.com
Dear Prof. Spoel,
Firstly, thanks for your reply.
I looked at the paper your said.
1.) To calculate the density d in a constant pressure simulation (in npt
simulation):
d=M/V equation (5)
M: mass of the system
V:volume of the system
Doesnt this formula (equation 5) use when Gromacs calculates the
Alternatively, has anyone else reproduced the viscosity calculation, or
tried to?
If anyone would be so kind as to forward their input files, that might help
me narrow down the problem with my own input files.
Thank you.
James
On 11 April 2013 16:55, James Cannon
Hi,
yes Marc you are right but the last time I used gromacs on a namd
trajectory
I noticed that time in the output files is useless 'cause it is always 0.
I understand that, since this information is usually took from .trr or
.xtc, it cannot
be extracted from a .dcd, but it could be more useful
Thank you all.
Would you suggest any link to a script like amb2gmx.pl ? I cannot fina
anything like this - basically I wish to convert top.prmtop to top.tpr.
On Tue, Apr 16, 2013 at 9:26 AM, francesco oteri
francesco.ot...@gmail.comwrote:
Hi,
yes Marc you are right but the last time I used
Hello:
I obtained a POPC lipids from CHARMM-GUI and I found the initial 12
line are following:
following atom name order:
ATOM 6315 N POPC 22 3.580 -22.614 19.970 1.00-19.29 MEMB
ATOM 6316 C12 POPC 22 4.563 -22.414 18.821 1.00-17.85 MEMB
ATOM 6317
On 4/16/13 5:32 AM, Steven Neumann wrote:
Thank you all.
Would you suggest any link to a script like amb2gmx.pl ? I cannot fina
anything like this - basically I wish to convert top.prmtop to top.tpr.
You will not be able to produce a .tpr file directly. The amb2gmx script simply
Got this.
Thank you
On Tue, Apr 16, 2013 at 11:21 AM, Justin Lemkul jalem...@vt.edu wrote:
On 4/16/13 5:32 AM, Steven Neumann wrote:
Thank you all.
Would you suggest any link to a script like amb2gmx.pl ? I cannot fina
anything like this - basically I wish to convert top.prmtop to
Dear all,
I am trying to do some two phase simulations with Decane molecules and some
other smaller molecules.
When I did simulations with smaller molecules, I specifies the properties
based on each atom, while I just realized it is really not desirable to do
it with Decane molecules ( 34 atoms
On 4/16/13 6:51 AM, Bao Kai wrote:
Dear all,
I am trying to do some two phase simulations with Decane molecules and some
other smaller molecules.
When I did simulations with smaller molecules, I specifies the properties
based on each atom, while I just realized it is really not desirable to
Dear GROMACS users,
Hi.
I want to study different protein-drug complexes and I follow the procedure
mentioned in the
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/.
I copied and pasted the positions of each drug to the end of conf.gro and did
other steps. Is
On 4/16/13 9:07 AM, Group Gro wrote:
Dear GROMACS users,
Hi.
I want to study different protein-drug complexes and I follow the procedure
mentioned in the
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/.
I copied and pasted the positions of each drug to the
I have a series of commands which I want to run a simulation. Is there a
way I can issue them together at the start such that the second command is
automatically executed after the first one finishes and so on without any
manual input.
Thanks in advance.
--
gmx-users mailing list
On 4/16/13 10:52 AM, Abhinav Agrawal wrote:
I have a series of commands which I want to run a simulation. Is there a
way I can issue them together at the start such that the second command is
automatically executed after the first one finishes and so on without any
manual input.
Just list
See style 8 for trjconv -h
Mark
On Tue, Apr 16, 2013 at 10:26 AM, francesco oteri francesco.ot...@gmail.com
wrote:
Hi,
yes Marc you are right but the last time I used gromacs on a namd
trajectory
I noticed that time in the output files is useless 'cause it is always 0.
I understand that,
Hello:
I've built a system with CHARMM-GUI, and I am trying to mimize it with
following em.mdp file
title = steepest descent energy minimization
define = -DPOSRES -DPOSRES_LIG
cpp = /usr/bin/cpp
include =
integrator = steep
On 4/16/13 1:05 PM, Albert wrote:
Hello:
I've built a system with CHARMM-GUI, and I am trying to mimize it with
following em.mdp file
title = steepest descent energy minimization
define = -DPOSRES -DPOSRES_LIG
cpp = /usr/bin/cpp
include
Hi Justin:
thanks for kind reply.
Yes, there many atom clashes in CHARMM-GUI system, so I add very
strong force on protein and ligands, and try to minimize the rest of the
system
do you have any idea how can I solve the issue and make it work?
thanks a lot
Albert
On 04/16/2013 07:09
On 4/16/13 1:13 PM, Albert wrote:
Hi Justin:
thanks for kind reply.
Yes, there many atom clashes in CHARMM-GUI system, so I add very strong force
on protein and ligands, and try to minimize the rest of the system
do you have any idea how can I solve the issue and make it work?
On 04/16/2013 07:28 PM, Justin Lemkul wrote:
Create a more physically reasonable starting structure.
-Justin
the protein and ligand are already minimized, but CHARMM-GUI create the
mix lipids automatically which I cannot change them.
ALBERT
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gmx-users mailing list
On 4/16/13 1:31 PM, Albert wrote:
On 04/16/2013 07:28 PM, Justin Lemkul wrote:
Create a more physically reasonable starting structure.
-Justin
the protein and ligand are already minimized, but CHARMM-GUI create the mix
lipids automatically which I cannot change them.
Then you will
Hello,I have had the same problem with CHARMM-GUI however I have found a
decent work-around procedure: 1. Go to your input .gro file and locate the
atom with infinite force (atom 23533 in this case)2. Change one of the x,y,z
positions of that atom by about /- 0.5.3. Rerun grompp with the new
Dear users,
g_analyze -f rmsd.xvg -av average.xvg -errbar stddev
Unfortunately, this command didn't produce the error bar
How can I obtain error bar for plotting?
Thanks in advance
--
Ahmet Yıldırım
--
gmx-users mailing listgmx-users@gromacs.org
On 4/16/13 4:26 PM, Ahmet yıldırım wrote:
Dear users,
g_analyze -f rmsd.xvg -av average.xvg -errbar stddev
Unfortunately, this command didn't produce the error bar
How can I obtain error bar for plotting?
Works fine for me. Perhaps you're just not plotting average.xvg correctly.
Import
First column is time, second is rmsd value and third column is 0.
average.xvg
10 0.3123 0
20 0.3256 0
30 0.3981 0
40 0.3512 0
50 0.3754 0
...
2013/4/16 Justin Lemkul jalem...@vt.edu
On 4/16/13 4:26 PM, Ahmet yıldırım wrote:
Dear users,
g_analyze -f rmsd.xvg -av average.xvg -errbar stddev
On Apr 16, 2013 6:28 AM, Albert mailmd2...@gmail.com wrote:
Hello:
I obtained a POPC lipids from CHARMM-GUI and I found the initial 12
line are following:
following atom name order:
ATOM 6315 N POPC 22 3.580 -22.614 19.970 1.00-19.29
MEMB
ATOM 6316 C12 POPC 22
On 4/16/13 6:50 PM, Mark Abraham wrote:
On Apr 16, 2013 6:28 AM, Albert mailmd2...@gmail.com wrote:
Hello:
I obtained a POPC lipids from CHARMM-GUI and I found the initial 12
line are following:
following atom name order:
ATOM 6315 N POPC 22 3.580 -22.614 19.970
On 4/16/13 4:47 PM, Ahmet yıldırım wrote:
First column is time, second is rmsd value and third column is 0.
average.xvg
10 0.3123 0
20 0.3256 0
30 0.3981 0
40 0.3512 0
50 0.3754 0
...
I see. It seems that g_analyze deals well with some files and not others. If,
for instance, I analyze a
Dear,
In my system ,the loop is part of the active pocket of the protein.
when the ligand is absent, the loop is disordered and if the ligand is present
, the loop can transform into helix. i don't know how to the simulate the state
of the shape of the loop at the different the
On 4/16/13 9:15 PM, aixintiankong wrote:
Dear,
In my system ,the loop is part of the active pocket of the protein.
when the ligand is absent, the loop is disordered and if the ligand is present
, the loop can transform into helix. i don't know how to the simulate the state
of the
Hello Mark and Justin:
thanks a lot for kind comments.
I changed the atom order in forcecfiled .rtp file so that they are the
same with the output from CHARMM-GUI, and it works fine now.
best
Albert
On 04/17/2013 12:50 AM, Mark Abraham wrote:
Support is not really the right word:-).
Hello Brad:
thanks for advices.
I've also solved the problem after I run the 6.1 minimization step in
NAMD. After that, I reimport the lipids system into gromacs, and it no
longer complain those issue.
best
Albert
On 04/16/2013 09:59 PM, Brad Van Oosten wrote:
Hello,I have had the
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