Dear all,
I want to study a system consisting of water, methane and CO2. I will
use TIP4P/Ice , OPLSAA and EPM2 models respectively for the components .
My problem is, how do I make a choice of the cutoff lengths, for a
system which uses different molecular models which were
Hi,
First of all, are you sure that you extended 2.xtc from 40ns?
Can you post your trjcat output, which shows the starting frame of each
trajectory.
It should be like as shown below
Summary of files and start times used:
FileStart time Time step
Thank you Justin!
I understand usually for regular equilibration, restraints should be enough.
But I am still wondering to what extent position restraint can restrain my
atoms. In fact, I ran a relatively longer NVT using position restraints and
I saw that both the absolute coordinates of my
Hello Venkat,
Ya, I am sure that I use 1st.cpt to run next 40 ns job
Find below the output of trjcat
Summary of files and start times used:
FileStart time Time step
-
complex_prod1_old.xtc0.000
So, that is the problem. Your second trajectory also has the same start
time. Some how you didn't extend your second run from where your 1st run
has finished.
Out of curiosity, why is your time step 50ps? Its too big for a simulation.
Generally it should be 2fs.
On Mon, Apr 21, 2014 at 12:30
You're just trying to measure a potential energy, so do it the right way
and don't get involved wiht making mistakes trying to freeze atoms. See
http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
Mark
On Mon, Apr 21, 2014 at 7:38 AM, sukriti002 sukriti...@e.ntu.edu.sg wrote:
Hi
Dear Sunita
Are you sure you have added two trajectory files, one from 0 to 40 and the
other from 40 onward ! Because
Here
*Summary of files and start times used: FileStart
time Time
step-
If you want to share a file, please use a file sharing service and share
the link.
Mark
On Mon, Apr 21, 2014 at 7:32 AM, sunita gupta sunita@gmail.com wrote:
Hello Everyone,
I have two trajectories of 40 ns each, the first one is from 0 to 40 ns and
next one is extended to next 40 ns
Hi Tsjerk,
Sorry for the confusion. I thought its time step which is actually
output writing frequency. Thank you sir for the correction.
On Mon, Apr 21, 2014 at 2:39 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Venkat,
That time step is the time step in the output trajectory. Yours
Dear Gromacs users
I would like to know whether you have ever run a simulation with
constraints in all-angles, or if you know about somebody who did it.
When I try to run a protein with this option, it crashes, and only
artificial systems like linear chains or modified small molecules seem
to
Hi All,
I have a membrane-protein-solvent system, and I want the potential across
the membrane in the direction of the membrane normal. I have 2 questions in
that regard.
1) We know that epsilon_r = 80 for the water, ~7 for the membrane-water
interface and ~2 for the hydrophobic membrane core.
If you can rule out file permissions issues (because you wrote files
earlier), and actually running out of disk, usually that would suggest a
flaky network file system.
Mark
On Mon, Apr 21, 2014 at 4:09 PM, Andrew Bostick
andrew.bosti...@gmail.comwrote:
Dear gromacs users
I am doing md
Dear all,
I noticed that Gromacs has the option to do Brownian Dynamics, is there anyone
who has done that or where can I find any tutorials that can teach me to do it?
Thanks.
Sincerely
Yutian (Shirley) Yang
Biomedical and Chemical Engineering
329 Link Hall Syracuse University
Syracuse NY
Dear Gromacs Users,
Is there a way to constrain or fix Center of Mass
of lipid bilayer or proteins in a MD run?
Thanks!
Thomas
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Dear Mark
Thanks for your reply.
I am beginner in linux and gromacs.
How to rule out file permissions issues? Which command is true for doing
this?
Please guide me to solve this problem.
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Did earlier frames get written? Use ls -l, gmxcheck etc. Google about file
permissions - unlike on (say) an old Windows machine, on a compute cluster
you will not be able to write files anywhere but where you're allowed to.
Guessing here, because you haven't supplied any context.
Mark
On Mon,
On 4/21/14, 9:58 AM, rajat desikan wrote:
Hi All,
I have a membrane-protein-solvent system, and I want the potential across
the membrane in the direction of the membrane normal. I have 2 questions in
that regard.
1) We know that epsilon_r = 80 for the water, ~7 for the membrane-water
On 4/21/14, 12:23 PM, Tom wrote:
Dear Gromacs Users,
Is there a way to constrain or fix Center of Mass
of lipid bilayer or proteins in a MD run?
To fix the position of the COM, use nstcomm = 1 (but your performance may suffer
badly), otherwise removal of COM drift periodically is handled
Please ask usage questions on the gmx-users mailing list. The development list
is for coding and planning discussions; this post is not appropriate here. I am
CC'ing this message over to gmx-users. Please post anything further there.
On 4/21/14, 10:28 AM, MOHD HOMAIDUR RAHMAN wrote:
Dear
Hi Justin,
So different parts of my system in Z-direction should be scaled
differently, right? On a coarse level, aqueous part with a scaling of 80,
membrane with a scaling of 2? How do I correct for this? Can I take the
quantitative output for potential difference across a membrane in water
from
On 4/21/14, 5:11 PM, rajat desikan wrote:
Hi Justin,
So different parts of my system in Z-direction should be scaled
differently, right? On a coarse level, aqueous part with a scaling of 80,
membrane with a scaling of 2? How do I correct for this? Can I take the
quantitative output for
On 4/21/14, 5:48 PM, mirc...@sjtu.edu.cn wrote:
Hi everyone,
I am using GROMACS to simulate bilayers, and I am testing two sets of
parameters at present. However, I found significant differences of simulation
speed of these two parameters sets.
The mainly differences between these
Dear Mark
Thanks for your reply.
I googled file permission in linux OS. After that I did following steps:
I created a directory entitled input.
I put pdb and mdp files in the input directory.
I used following command to change permission:
chmod -R 777 input
Now I will md simulation steps
Hello Venkat,
Yeah, I think by default it will give 0 ps as start time for both
trajectories and it should be set by user using -settime flag
Correct me if I am wrong.
Regards
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