Hi Justin,
Thanks Justion for replying. I am currently simulating only 1 SWM4 water
molecule and I am getting a few errors.
I just want to clear up a few things below.
_
*1.* when I run pdb2gmx with this .rtp file
[ SM2 ]
[
Yes. Or you could have tried it to see! :-)
Mark
On Feb 22, 2014 8:04 AM, Yogendra Ramtirtha ramtirtha.yogen...@gmail.com
wrote:
Actually, I used the build directory which was created earlier.
Should I create a new build directory all over again ?
Can you please guide me.
Thanks
On Sat,
Thanks, I will try it all over again :)
On Sat, Feb 22, 2014 at 3:49 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
Yes. Or you could have tried it to see! :-)
Mark
On Feb 22, 2014 8:04 AM, Yogendra Ramtirtha
ramtirtha.yogen...@gmail.com
wrote:
Actually, I used the build directory
Dear gromacs users,
I have got two phosphorylated residues Tyrosine (TPO) and Serine (SEP) in A
and B chains of my heterotrimer homology model. So, I went with the step by
step process suggested by GROMACS at the
link:http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
On 2/22/14, 5:44 AM, Dr. Vitaly Chaban wrote:
g_energy
...and a three rounds of g_sas to get protein, CNT, then protein+CNT surface
area to calculate the interfacial area.
-Justin
On Sat, Feb 22, 2014 at 8:06 AM, maryam haji maryam6...@gmail.com wrote:
I am doing simulation of the
On 2/22/14, 6:31 AM, lalithkumar wrote:
Dear gromacs users,
I have got two phosphorylated residues Tyrosine (TPO) and Serine (SEP) in A
and B chains of my heterotrimer homology model. So, I went with the step by
step process suggested by GROMACS at the
Dear all,
I have been having some puzzling results when using g_sas to analyze some
trajectories, so I have decided to go back to basics.
As described in the documentation, g_sas implements the double cubic
lattice method (DCLM) originally presented in Eisenhaber1995 (doi:
10.1002/jcc.540160303
Hi All,
I have simulated a membrane proteins system using coarse grain model. after
simulations when i removed periodic boundary from my simulations box but
the protein is moving up and down in the box ? I have tried all the
options nojump ,mol,whole ...etc. no options seems to work.
there is
On 2/22/14, 12:43 PM, Nikhil Agrawal wrote:
Hi All,
I have simulated a membrane proteins system using coarse grain model. after
simulations when i removed periodic boundary from my simulations box but
the protein is moving up and down in the box ? I have tried all the
options nojump
it has nothing to do with CG description of PES.
try the option of trjconv, which is to make molecules whole again
Dr. Vitaly V. Chaban
On Sat, Feb 22, 2014 at 6:43 PM, Nikhil Agrawal nikhil.08...@gmail.com wrote:
Hi All,
I have simulated a membrane proteins system using coarse grain model.
On 2014-02-22 18:34, João M. Damas wrote:
Dear all,
I have been having some puzzling results when using g_sas to analyze some
trajectories, so I have decided to go back to basics.
As described in the documentation, g_sas implements the double cubic
lattice method (DCLM) originally presented in
I do not know what the manual says, but if you are talking about
viscosity computation through cos-like acceleration, then g_energy is
doing all the work for you.
Dr. Vitaly V. Chaban
On Fri, Feb 21, 2014 at 10:38 PM, Marcelo Vanean vanea...@gmail.com wrote:
I am trying to calculate the
Dr. Vitaly Chaban, I know that g_energy is doing all the work for me.
However I want to understand the concepts.
On Fri, Feb 21, 2014 at 6:38 PM, Marcelo Vanean vanea...@gmail.com wrote:
I am trying to calculate the viscosity of water (spc model) by periodic
perturbation method. The manual
See the following for more information:
Effects of Temperature Control Algorithms on Transport Properties and
Kinetics in Molecular Dynamics Simulations
http://pubs.acs.org/doi/abs/10.1021/ct400109a
When discussing velocity profile, I believe this is referring to any
external driving force that
On Sat, Feb 22, 2014 at 10:16 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:
The workaround is to trjconv -o 111.pdb, open an editor, select a
block of coordinates, and paste in XYZ file.
I also do not like PDB files from gromacs, but AFAIK many programs
generate such PDB files which other
Vitaly V. Chaban, this is the question. How to remove the heat
generated by viscous friction by heat bath without coupling the
velocity profile to heat bath? Also, why to remove the velocity
profile of the kinetic energy?
On Sat, Feb 22, 2014 at 9:08 PM, Marcelo Vanean vanea...@gmail.com wrote:
I'm pretty sure that viscous friction is not what is referred to when
it's talking about a velocity profile; it's the COM velocities.
On Sat, Feb 22, 2014 at 7:46 PM, Marcelo Vanean vanea...@gmail.com wrote:
Vitaly V. Chaban, this is the question. How to remove the heat
generated by viscous
Michael Shirts, the manual says (manual 4.6.5, pages 169 - 170): To
obtain the correct value for the viscosity the generated velocity
profile should not be coupled to the heat bath, also the velocity
profile should be excluded from the kinetic energy and The heat
generated by the viscous friction
Hello David,
Thank you for your fast reply and your suggestions! The results are in
Attached Table 2 (see below).
- I followed your PBC suggestion, but used the -pbc flag instead (I
still ended up doing yours, read further ahead). While turning off PBC for
GMX4.0.4 leaves the results
Update for anyone interested: Installing dssp 2.2.1 solved the above error!
I am not sure why...
On Sun, Feb 9, 2014 at 11:39 AM, rajat desikan rajatdesi...@gmail.comwrote:
Hi All,
I get this error while running do_dssp. The program reads the whole
trajectory but fails to write a scount
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