Hi Justin,
I completely dazed over the "download .tgz" option at the top right of the
screen. I got all of the files I need for my membrane. Thank you!
*Sanim Rahman*
On Sat, Mar 18, 2017 at 8:03 AM, Justin Lemkul wrote:
>
>
> On 3/18/17 1:25 AM, Sanim Rahman wrote:
>
>> Sorry I found this th
Hi,
You haven't done a simulation, you've moved down a potential energy surface
from one point to another. Of course the potential energy deviates. How
much depends how far away from something reasonable you were when you
started :-)
Mark
On Sun, Mar 19, 2017 at 2:19 AM Mishelle Oña wrote:
> T
On 3/18/17 9:18 PM, Mishelle Oña wrote:
Thanks for your answer Justin.
Another question for the same simulation. I got this values of potential energy:
Average> -127776
Err.Est.>4900
RMSD>12891.3
Tot-Drift> -32877.9
I think the RMSD is way too high. What do you think?
Consider the name
Thanks for your answer Justin.
Another question for the same simulation. I got this values of potential energy:
Average> -127776
Err.Est.>4900
RMSD>12891.3
Tot-Drift> -32877.9
I think the RMSD is way too high. What do you think?
From: gromacs.org_gmx-users-bo
On 3/18/17 9:00 PM, Mishelle Oña wrote:
Hello!
I have a question about pressure in EM simulation. I am using Steepest descent
method in a water polymer system. My pressure gets this value:
Energy Average Err.Est. RMSD Tot-Drift
--
Hello!
I have a question about pressure in EM simulation. I am using Steepest descent
method in a water polymer system. My pressure gets this value:
Energy Average Err.Est. RMSD Tot-Drift
--
Dear all,
I would like to calculate surface tension/pressure of my monolayer
simulation. I have two monolayers of lipid each side of a water box. So
four interfaces; vaccum/lipid, lipid/water, water/lipid and lipid/vaccum. I
used NVT simulation. Is there a way to calculate surface tension/pressure
On 3/18/17 7:36 AM, Rakesh Pant wrote:
Dear Justin,
Could you briefly tell how the vibrational analysis is done. Which method
and software is generally used.
The primary literature for the chosen force field should have this information.
-Justin
Thanks
Rakesh
On Fri, Mar 17, 2017 at 7:1
On 3/18/17 6:46 AM, Juan José Galano Frutos wrote:
On 3/17/17 10:35 AM, Juan José Galano Frutos wrote:
* Thank you Justin for your replay. I've read that to compute specific
*>* heats (Cv or Cp) it is necessary calculating quantum correction (using
*>* the tool g_nmeig).
*>* Then, this tool c
On 3/18/17 6:27 AM, Anurag Kumar wrote:
Dear all,
Restraining dihedral for dipeptide in explicit water model, how it can be
done?
There are lots of threads in the archive about this (Google is your friend) as
well as relevant topology and .mdp options in the manual.
-Justin
--
=
On 3/18/17 1:25 AM, Sanim Rahman wrote:
Sorry I found this thread here:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-September/108197.html
From my understanding, I use pdb2gmx on my entire output file, however,
where does the data in the .psf file go?
You shouldn't be
On 3/17/17 12:43 PM, Vignesh Waran wrote:
respected sir,
i am using protein-ligand complex tutorials .this my problem .i have all
process has been done but like energy minimization result is not coming
what we do sir ?
my command line gmx mdrun -v -deffnm em
how to find the clarify the
Dear Justin,
Could you briefly tell how the vibrational analysis is done. Which method
and software is generally used.
Thanks
Rakesh
On Fri, Mar 17, 2017 at 7:16 PM, Justin Lemkul wrote:
>
>
> On 3/17/17 7:53 AM, Rakesh Pant wrote:
>
>> Dear all,
>>
>> How to calculate force constant for bonds
On 3/17/17 10:35 AM, Juan José Galano Frutos wrote:
>* Thank you Justin for your replay. I've read that to compute specific
*>* heats (Cv or Cp) it is necessary calculating quantum correction (using
*>* the tool g_nmeig).
*>* Then, this tool calculates such a correction using the Hessian matrix.
*>
Dear all,
Restraining dihedral for dipeptide in explicit water model, how it can be
done?
Thank you,
Anurag Kumar
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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espected sir,
i am using protein-ligand complex tutorials .this my problem .i have all
process has been done but like energy minimization result is not coming
what we do sir ?
my command line gmx mdrun -v -deffnm em
how to find the clarify the problem?
pls tell me sir
GROMACS: gmx m
espected sir,
i am using protein-ligand complex tutorials .this my problem .i have all
process has been done but like energy minimization result is not coming
what we do sir ?
my command line gmx mdrun -v -deffnm em
how to find the clarify the problem?
pls tell me sir
GROMACS: gmx m
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