Dear Gromacs users,
I have downloaded the POPC bilayer molecular coordinates with charmmff
equilibrated from Dr. Klauda's website. In this site it is mentioned
Note: If you run these simulations in NAMD you MUST use NAMD 2.7b3
with vdw ForceSwitching turned on;
what does vdw ForceSwitching turne
Samrat Pal wrote:
Hi Justin,
No. I have not added any ions.
Well, then it's a complete mystery. You'll have to go through your coordinate
file and topology and count the relevant number of molecules or atoms and decide
for yourself where the mismatch comes from. Nothing that you've provid
Hi Justin,
No. I have not added any ions.
Samrat
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Friday, October 21, 2011 11:39 AM
Subject: Re: [gmx-users] mismatch in coordinate and topology
Samrat Pal wrote:
> Hi Justin,
> (1) Non
James Starlight wrote:
Justin,
So It seems that I've done all steps in accordance to that workflow and
there have not been any more errors during loading my system in the
gromp. :)
By the way I have some methodological questions
1- Could you provide me with the source of the initial si
vidhya sankar wrote:
Dear Justin Thank you for your previous reply.
As u mailed me already g_mindist of gromacs is the best tool to study
about Hydrophobic contacts.
>From this i got only Average number of contacts.
Samrat Pal wrote:
Hi Justin,
(1) None of the ligands have 31 atoms - FAD has 86 atoms and MHF has 54
atoms. The error msg. does not show any specific mismatching.
(2) I forgot to mention that I have increased the number of the atoms on
the top (2nd line) of the gro file after addin
Justin,
So It seems that I've done all steps in accordance to that workflow and
there have not been any more errors during loading my system in the gromp.
:)
By the way I have some methodological questions
1- Could you provide me with the source of the initial single lipids?
Previously I've d
Dear Justin Thank you for your previous reply.
As u
mailed me already g_mindist of gromacs is the best tool to study about
Hydrophobic contacts.
From this i got only Average number of contacts. But i need the free energy
Hi Justin,
(1) None of the ligands have 31 atoms - FAD has 86 atoms and MHF has 54 atoms.
The error msg. does not show any specific mismatching.
(2) I forgot to mention that I have increased the number of the atoms on the
top (2nd line) of the gro file after adding the 2 ligands.
Sam
Samrat Pal wrote:
Hi All,
I am trying to minimize the chryptochrome structure that has
one FAD and one MHF ligand bound to it.
Following are the steps that I performed
(1) Created the protein coordinate(gro) file using pdb2gmx command and
choosing GROMOS43a1 force-field
(2
Hi All,
I am trying to minimize the chryptochrome structure that has one FAD
and one MHF ligand bound to it.
Following are the steps that I performed
(1) Created the protein coordinate(gro) file using pdb2gmx command and choosing
GROMOS43a1 force-field
(2) Created the FAD and
On 21/10/2011 10:49 PM, Chandan Choudhury wrote:
Hi gmx-users,
Is it possible to extend a simulation with change in the output
control parameter (nstxtcout)?
Yes, but not with tpbconv. Take your original .mdp file, change what you
want, invoke grompp the same way. You can either give the che
James Starlight wrote:
So I should to use topol.top obtained for 1 lipid as the lipid.itp for
the sustem contained of the same lipids, shouldnt I?
A .top can be converted to a .itp which can then be included in a real system
.top topology. So the lipid .top that you receive from pdb2gmx s
So I should to use topol.top obtained for 1 lipid as the lipid.itp for the
sustem contained of the same lipids, shouldnt I?
2011/10/21 Justin A. Lemkul
>
>
> James Starlight wrote:
>
>> Justin,
>>
>> In that way there was only one point wich was not understood for me
>>
>>
>> In charmm I already
James Starlight wrote:
Justin,
In that way there was only one point wich was not understood for me
In charmm I already have lipids.rtp with the parametries for my lipids.
Also I have a single molecule of my lipid.
How via pdb2gmx I could create parametrised itp file except of posre.itp ?
Justin,
In that way there was only one point wich was not understood for me
In charmm I already have lipids.rtp with the parametries for my lipids. Also
I have a single molecule of my lipid.
How via pdb2gmx I could create parametrised itp file except of posre.itp ?
James
2011/10/21 Justin A. L
Natalie Stephenson wrote:
Hi Justin (and gmx-users),
I've been looking into using g_sham for the free energy landscapes, however
I'm not sure what variables I should plot ... could I just use the g_energy
(potential) outputs to produce the energy landscape?? Other examples I've
seen using g_s
You'll learn far more by discovering it yourself.
I stand by this statement. Perhaps some kind person with sufficient time on
their hands will do your literature searching for you, but I do not, sorry. The
information you need is out there. Start with the primary citation for whatever
James Starlight wrote:
I've excluded "charmm36.ff/lipids.rtp" from my topology and obtain new
error
Fatal error:
No such moleculetype POPC
How I could include topology on this lipids ( all of them are present in
the lipids.rtp. ) ?
I have itp for the lipids only for the GROMOS ff so it sho
madhumita das wrote:
Hi GROMACS users,
I have generated topology and gromacs files using acpype.py .This is a
membrane protein and thus to be simulated along with membrane. How can I
use AMBER forcefield instead of GROMOS force field. Should I do the
same as stated in the GROMACS tutorial
Hi gmx-users,
Is it possible to extend a simulation with change in the output control
parameter (nstxtcout)?
I am aware of that tpbconv can extend a simulation with the same output
controls as in the input tpr file.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
--
gmx-users mailing list
Hi GROMACS users,
I have generated topology and gromacs files using acpype.py .This is a
membrane protein and thus to be simulated along with membrane. How can I use
AMBER forcefield instead of GROMOS force field. Should I do the same as
stated in the GROMACS tutorial in which GROMOS force field
I've excluded "charmm36.ff/lipids.rtp" from my topology and obtain new
error
Fatal error:
No such moleculetype POPC
How I could include topology on this lipids ( all of them are present in the
lipids.rtp. ) ?
I have itp for the lipids only for the GROMOS ff so it should not be used
here
James
Dear Pratik,
>
>
> I am trying to create the tip6p itp file. In order to do that, since
> it is an overlap of the tip4p and tip5p model (visually)
> I am trying to understand the a, b, and c values for the position of
> the dummy charge in the tip5p models.
>
> Below is the part of the script
To whomsoever it may concern,
I am trying to create the tip6p itp file. In order to do that, since it is an
overlap of the tip4p and tip5p model (visually)
I am trying to understand the a, b, and c values for the position of the dummy
charge in the tip5p models.
Below is the part of the scri
To whomsoever it may concern,
I am trying to create the tip6p itp file. In order to do that, since it is an
overlap of the tip4p and tip5p model (visually)
I am trying to understand the a, b, and c values for the position of the dummy
charge in the tip5p models.
Below is the part of the scri
Hi Justin (and gmx-users),
I've been looking into using g_sham for the free energy landscapes, however I'm
not sure what variables I should plot ... could I just use the g_energy
(potential) outputs to produce the energy landscape?? Other examples I've seen
using g_sham have done quite in dept
Dear Gmx Users,
I run the simulation of my protein and ligands. I specified the energy
groups of each of the residue of my protein. I would like to calculate the
total interaction energy:
V=V(electr)+V(vdw) for each residue and my ligands as a function of the
distance between them.
I am intereste
Justin, thanks again for the information
Different force fields require different settings, most notably cutoffs.
> Understanding the intrinsics of the chosen force field is a prerequisite for
> using it. Again, time spent in the literature here is more valuable than me
> spitting out settings t
After running this minimization when i did gmxcheck i got this output
trn version: GMX_trn_file (single precision)
Reading frame 0 time9.000
# Atoms 4113
Reading frame 3 time 57.000
Timesteps at t=31 don't match (12, 26)
Reading frame 4 time 69.000
Timesteps at t=57 don'
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