On 28/12/2011 6:59 PM, leila karami wrote:
Dear Mark
thanks for your reply.
I have a general questions:
For what parameters I can use g_analyze -av average.xvg -errbar stddev -f
*.xvg?//
//*** What quantity do you wish to show with an error bar?
I want to show output from g_dist with an
Dear Mark
I am studying interaction between protein and dna, especially hydrogen
bonds. using g-dist, I obtained distance between donor atom of protein and
acceptor atom of dna.
in this case, can I use g_analyze for obtaining error bar or stddev?
--
gmx-users mailing list
Thank you very much for your advice... I have tried including dispcorr =
enerpres in my mdp file and the density increased a bit in a timescale of 5
ns but it is still far from the value expected for pure water. These are
the new results:
Statistics over 251 steps [ 0. thru 5000. ps
Dear Mark
can I obtain error bar twice the standard error of the average
distance between the donor atom of protein and acceptor atom of dna over 1
simulation?
should I do several simulation. Is 1 simulation enough?
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gmx-users mailing listgmx-users@gromacs.org
- Forwarded Message -
From: mohammad agha mra...@yahoo.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tuesday, December 27, 2011 8:59 PM
Subject: Re: [gmx-users] trjconv and g_clustsize
Thank you very much from your reply.
I found out that my problem is at
Hi
I just saw the article Temperature Dependence of TIP3P, SPC, and TIP4P
Water from NPT Monte Carlo Simulations: Seeking Temperatures of Maximum
Density published in Journal of Computational Chemistry, Vol. 19, No. 10,
1179]1186 (1998). It gives 0.985 for SPC at 25 C with different setup...
how to use gromacs 4.5.5's temple
Dear teacher,
i have already modify the code, and also make it.
Attached is my modified code good.
Dear teacher,
how to use gromacs 4.5.5's temple?
I expect that it is not meant to be functional. It's meant to be a
template from which you can write
Hello Gromacs users,
I'm using a Buckingham potential for the nonbonded interactions in my
system, so I have the following lines in my forcefield.itp file:
[ defaults ]
; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ
2 1 no 1.0
I apologize for the truncated message; I pressed send too soon.
According to the Gromacs manual, pairs cannot be generated automatically
for the Buckingham potential, but the [ pairtypes ] directive seems to only
accept parameters in LJ form (i.e. c6 and c12, instead of a, b, and c6).
I've been
Dear GROMACS users,
I have a problem
about trjconv -pbc nojump, I have 2 micelles in the end of my simulation.
For analysis I should do three steps for micelle clustering at
http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering?highlight=micelle+clustering
Steps 1 and 2 work good and
I have been trying to set up simulation between 10 molecules of taurine with
lysolecithin stearoyl, i generated the topology files with PRODRG but i s
haven't managed to run the equilibrium. The error i recieve says there's a
problem with the position restrain files.
What can i do?
Thanks in
Hovakim Grabski wrote:
I have been trying to set up simulation between 10 molecules of taurine
with lysolecithin stearoyl, i generated the topology files with PRODRG
but i s haven't managed to run the equilibrium. The error i recieve says
there's a problem with the position restrain files.
Hi Sara,
The problem is that your micelle is formed at the end of the
trajectory. To get what you want, you need to mirror the trajectory,
follow the procedure you followed, and mirror the resulting
trajectory. I posted a piece of python code for mirroring a trajectory
a while back:
On 12/17/11, Saba Ferdous saba.bsbi...@iiu.edu.pk wrote:
Dear Gromacs experts,
I want to ask about coulomb energies. Like if coulomb-SR and coulomb-14
show high RMSD then what should we interpret from such results??
Average Coulomb Energy (kJ/mol)
-1.62657e+06
RMSD
2236.85
Error
afsaneh maleki wrote:
On 12/17/11, Saba Ferdous saba.bsbi...@iiu.edu.pk wrote:
Dear Gromacs experts,
I want to ask about coulomb energies. Like if coulomb-SR and coulomb-14
show high RMSD then what should we interpret from such results??
Average Coulomb Energy (kJ/mol)
-1.62657e+06
RMSD
What performance are you getting that you want to improve more?
Here's a datapoint from the last simulation I ran:
Currently running gromacs 4.5.4 built with icc+fftw+openmpi on infiniband
qdr and I get about 9.7ns/day on 64 PP nodes with 4 PME nodes (68 total
2.66ghz X5650) on my 99113 atom
Hi Sara,
Please keep discussions on the list. I'm not your private tutor.
Whether you can do your analysis depends on the analysis you want to
do. But if your aim is analyzing the formation of the micelle, you're
probably better of reversing the trajectory.
1- trjconv -f md.trr -o md1.xtc -n
On 28/12/11, Theodora García theodoraaagar...@gmail.com wrote:
Hi
I just saw the article Temperature Dependence of TIP3P, SPC, and TIP4P Water
from NPT Monte Carlo Simulations: Seeking Temperatures of Maximum Density
published in Journal of Computational Chemistry, Vol. 19, No. 10,
On 29/12/11, Olivia Waring owar...@princeton.edu wrote:
I apologize for the truncated message; I pressed send too soon.
According to the Gromacs manual, pairs cannot be generated automatically for
the Buckingham potential,
Where does it say this?
but the [ pairtypes ]
On 28/12/11, 杜波 2008d...@gmail.com wrote:
how to use gromacs 4.5.5's temple
Dear teacher,
i have already modify the code, and also make it.
Attached is my modified code good.
As you will see in the template code's desc variable, the original version
needs to be told about
On 29/12/11, Peter C. Lai p...@uab.edu wrote:
What performance are you getting that you want to improve more?
Here's a datapoint from the last simulation I ran:
Currently running gromacs 4.5.4 built with icc+fftw+openmpi on infiniband
qdr and I get about 9.7ns/day on 64 PP nodes with 4
Thank you very much from your reply.
Best Regards
Sara
From: Tsjerk Wassenaar tsje...@gmail.com
To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users
gmx-users@gromacs.org
Sent: Thursday, December 29, 2011 1:56 AM
Subject: Re: [gmx-users] -pbc
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