With no [pairs] section, no 1-4 interactions are computed. Note that
gen-pairs=yes does not automatically identifies and add the 1-4 pairs in
your system, you need to specify them in the [pair] in your topology.
[pairtypes] contain the parameters to build the potential terms for the
pairs incl
Dear Help,
I am trying to run REMD simulations and found couple of interesting
discussions on GROMACS mailing list regarding ensembles which can be used
during REMD.
I will be running REMD of small peptide in explicit solvent and I am
confused about gen_temp and gen_vel parameters for these simul
I would like to analyze the different conformations (~1000 structures)
of a protein/protein complex using GROMACS. Can I list all of these pdb
files within a text file when I start the pdb2gmx; i.e., text file that
includes:
0001.pdb
0002.pdb
or is there any other ways to handle this prob
You could use a script to do all runs consecutively using one pdb file
at a time. Anyway, if what you have are different conformations of the
same system, the same topology should apply for all of them, so just
need to obtain it once.
Javier
El 16/01/13 12:07, Serdar Durdagi, PhD escribió:
I
Dear Justin Thank you for your Previous reply
I am Following your Protein Lipid Tutorial When I do the msd analysis For
protein in DPPC lipid-water Bilayer in lateral Z direction using P8 atoms as
index Then I have Got the Following Output Is the Following My Out put
is Reasonable o
On 1/16/13 6:18 AM, vidhya sankar wrote:
Dear Justin Thank you for your Previous reply
I am Following your Protein Lipid Tutorial When I do the msd analysis For
protein in DPPC lipid-water Bilayer in lateral Z direction using P8 atoms as
index Then I have Got the Following Output
Hi Ronald,
Using intel-suite/64/2013.0/079 with mkl with the release-4-6 branch
version:
f3dd8cb7ae23accff657551523d05657262a72ff
gave no compiler warnings for
$ export CC=icc ; export CXX=icpc ; cmake -DGMX_MPI=OFF
-DGMX_DOUBLE=ON -DGMX_GPU=OFF -DGMX_PREFER_STATIC_LIBS=ON
-DGMX_FFT_LIBR
Hi,
In my system, I have a special bond (isopeptide bond, i.e., a bond
between amino group of Lys and the carboxyl terminus of another
protein). Before the simulation, is this bond should be formed or both
LYS (which is defined with different residue name, e.g., LYX) and
carboxyl terminus of a
On 1/16/13 3:56 AM, Neha Gandhi wrote:
Dear Help,
I am trying to run REMD simulations and found couple of interesting
discussions on GROMACS mailing list regarding ensembles which can be used
during REMD.
I will be running REMD of small peptide in explicit solvent and I am
confused about gen_
On 1/16/13 6:54 AM, Serdar Durdagi, PhD wrote:
Hi,
In my system, I have a special bond (isopeptide bond, i.e., a bond between amino
group of Lys and the carboxyl terminus of another protein). Before the
simulation, is this bond should be formed or both LYS (which is defined with
different resid
On 1/16/13 5:32 AM, Devika N T wrote:
4.5.5 versio
Writing topology
Processing chain 2 'A' (4 atoms, 4 residues)
Warning: Starting residue CA149 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue CA150 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue CA1
Thank you Justin for your reply.
I need to perform the effect of Calcium (CA) with protein Calmodulin.
>From the warning message its clear that "CA" is not identified as ion.
But previously I tried the run with Gromacs version 4.0.7 at that time
Version 4.0.7
Warning: 'CA' not found in residue
On 1/16/13 7:38 AM, Devika N T wrote:
Thank you Justin for your reply.
I need to perform the effect of Calcium (CA) with protein Calmodulin.
From the warning message its clear that "CA" is not identified as ion.
But previously I tried the run with Gromacs version 4.0.7 at that time
Version
Thank you Justin for your valuable suggestion.
I will follow it up.
* Regards**
N.T. Devika*
On Wed, Jan 16, 2013 at 6:16 PM, Justin Lemkul wrote:
>
>
> On 1/16/13 7:38 AM, Devika N T wrote:
>
>> Thank you Justin for your reply.
>>
>> I need to perform the effect of Calcium (CA) with
Thanks, that's expected. We've fixed some issues here.
Mark
On Wed, Jan 16, 2013 at 12:22 PM, Richard Broadbent <
richard.broadben...@imperial.ac.uk> wrote:
> Hi Ronald,
>
> Using intel-suite/64/2013.0/079 with mkl with the release-4-6 branch
> version:
>
> f3dd8cb7ae23accff657551523d056**57262a
The GROMACS team has no plans for that. The usual problem here is that
everybody would like every algorithm included, but that developers with
time and experience are scarce :-) It's an open source project though, so
anyone can do whatever they like. We're prepared to consider inclusions to
the mai
Hi all!
I've also done some calculations with the SD integraator used as the
thermostat ( without t_coupl ) with the system of 65k atoms I obtained
10ns\day performance on gtc 670 and 4th core i5.
I haventrun any simulations with MD integrator yet so It should test it.
James
2013/1/15 Szilárd Pá
Hi,
Unfortunately this is not a bug, but a feature!
We made the non-bondeds so fast on the GPU that integration and constraints
take more time.
The sd1 integrator is almost as fast as the md integrator, but slightly less
accurate.
In most cases that's a good solution.
I closed the redmine issu
Dear All,
I performed a MD simulation of a protein into a rhombic dodecahedric
box. Now I'd need to convert this dodecahedric box into a triclinic one
(I mean, not only for one frame to obtain a .gro file, but for the
entire trajectory).
I think that it would be possible using trjconv command,
We should probably note this effect on the wiki somewhere?
Mark
On Wed, Jan 16, 2013 at 3:44 PM, Berk Hess wrote:
>
> Hi,
>
> Unfortunately this is not a bug, but a feature!
> We made the non-bondeds so fast on the GPU that integration and
> constraints take more time.
> The sd1 integrator is a
On 2013-01-16 16:03, Anna Marabotti wrote:
Dear All,
I performed a MD simulation of a protein into a rhombic dodecahedric
box. Now I'd need to convert this dodecahedric box into a triclinic one
(I mean, not only for one frame to obtain a .gro file, but for the
entire trajectory).
I think that it
The issue I'm referring to is about a factor of 2 in update and constraints,
but here it's much more.
I just found out that the SD update is not OpenMP threaded (and I even noted in
the code why this is).
I reopened the issue and will find a solution.
Cheers.
Berk
Hello all,
I have the same problem, but I think the dihedral is properly defined.
I am running a polymer with the G53A6 force field. First I use pdb2gmx to
generate a conf and a top file. When I run grompp, I have the error(s):
ERROR 1 [file topol.top, line 1507]:
No default Proper Dih. types
On 1/16/13 10:58 AM, escajarro wrote:
Hello all,
I have the same problem, but I think the dihedral is properly defined.
I am running a polymer with the G53A6 force field. First I use pdb2gmx to
generate a conf and a top file. When I run grompp, I have the error(s):
ERROR 1 [file topol.top, l
On 1/16/13 10:09 AM, Kieu Thu Nguyen wrote:
Dear All,
I want to merge two or many boxes with the same size into one new box. The
size of new box is not a multiples of old box size. And the molecules that
overlap have to be removed. In Gromacs, are there any tool for my problem ?
See the log
On Wed, Jan 16, 2013 at 8:37 AM, Marcelo Depolo wrote:
>
> I was minimizing my system (with only proteins) and i got this error in the
> log:
>
> *Polak-Ribiere Conjugate Gradients:
>Tolerance (Fmax) = 1.0e-01
>Number of steps= -1
>F-max = 4.76837e+04
Dear gmx users,
Background: I just finished my 100 ns md simulation on a receptor in membrane
and I got all my .trr .xtc and .edr output files
In order to calculate the energy potential only for the protein, I made a new
.mdp defining "energygrps : Protein", thus obtaining a new .tpr for a rer
You should try packmol software. You will need to use a pdb formats, but then
you transform to .gro with pdb2gmx. It´s free and very easy to use.
http://www.ime.unicamp.br/~martinez/packmol/
Flor
Dra.M.Florencia Martini
Cátedra de Farmacotecnia II
Facultad de Farmacia y Bioquímica
Universid
Thanks, Elton.
I appreciate your answer, but my question was about the Warning error. The
convergence value was set ok. The minimization do not go further because
the error:
*"WARNING: there may be something wrong with energy file prt_cg.edr
Found: step=-1, nre=36, nblock=0, time=-1.
Trying to sk
On Wed, Jan 16, 2013 at 3:11 PM, Marcelo Depolo wrote:
> Thanks, Elton.
>
> I appreciate your answer, but my question was about the Warning error. The
> convergence value was set ok. The minimization do not go further because
> the error:
>
> *"WARNING: there may be something wrong with energy fil
On 1/16/13 12:11 PM, Marcelo Depolo wrote:
Thanks, Elton.
I appreciate your answer, but my question was about the Warning error. The
convergence value was set ok. The minimization do not go further because
the error:
*"WARNING: there may be something wrong with energy file prt_cg.edr
Found: s
I have set nstenergy=100. I'm using gromacs compiled with double precision
and even so, the stepsize was too small.
i have faced this convergence problems earlier, and managed some solutions.
I'm really wondering about the warning part, that I have never seen.
--
Marcelo Depólo Polêto
--
gmx-user
Justin,
I'm using gromacs 4.5.5 version, compiled in double precision. I tried to
generate the .tpr file 3 times and got the same results. About the
gmxcheck, i don't know how to use it to check my .edr file.
How can I do this?
--
Marcelo Depólo Polêto
--
gmx-users mailing listgmx-users@grom
I assume PLUMED will be implemented for Gromacs 4.6, as many PLUMED
developers use Gromacs. Perhaps any PLUMED lurkers on the list can
speak up. . . .
On Wed, Jan 16, 2013 at 9:20 AM, Mark Abraham wrote:
> The GROMACS team has no plans for that. The usual problem here is that
> everybody would l
On 1/16/13 12:36 PM, Marcelo Depolo wrote:
Justin,
I'm using gromacs 4.5.5 version, compiled in double precision. I tried to
generate the .tpr file 3 times and got the same results. About the
gmxcheck, i don't know how to use it to check my .edr file.
How can I do this?
Start with reading
Thank Justin and Flor so much ! Sorry about my unclear question. I mean
that my boxes is not isotropic. Each box has many types of molecules such
as water, lipid, ... Are those tools that you adviced me available for this
problem ?
Regards,
KT
On Wed, Jan 16, 2013 at 11:46 PM, FLOR MARTINI wrot
Hi,
yes I can confirm you that PLUMED will be available for gromacs-4.6!
We are currently testing it.
Carlo
> Message: 6
> Date: Wed, 16 Jan 2013 12:54:11 -0500
> From: Michael Shirts
> Subject: Re: [gmx-users] meta-dynamics in gromacs-4.6
> To: Discussion list for GROMACS users
> Message-ID:
On 1/16/13 4:39 PM, Kieu Thu Nguyen wrote:
Thank Justin and Flor so much ! Sorry about my unclear question. I mean
that my boxes is not isotropic. Each box has many types of molecules such
as water, lipid, ... Are those tools that you adviced me available for this
problem ?
That depends on w
@Justin, i am trying to simulate oligomerization of membrane protein. I
want to assemble a big box with proteins from many small box having a
protein. Is it available ?
@Flor, thanks you so much for your advice. I will try, i hope it helpful :-)
On Thu, Jan 17, 2013 at 5:11 AM, Justin Lemkul wr
On 1/16/13 8:26 PM, Kieu Thu Nguyen wrote:
@Justin, i am trying to simulate oligomerization of membrane protein. I
want to assemble a big box with proteins from many small box having a
protein. Is it available ?
The method I described previously should work. You place one patch (membrane +
Hi,
I am recently trying to perform an umbrella sampling simulation along a
particular reaction coordinate on a system where I have also put position
restraint on certain atoms of the system... So, for each umbrella sampling
window, I have an extra potential on certain atoms ( due to the positi
Dear Bogdan Costescu,
Thank you for your valuable suggestion.
Regards,
Ramesh.
On Mon, Jan 14, 2013 at 8:20 PM, Bogdan Costescu wrote:
> On Sat, Jan 12, 2013 at 10:04 AM, ramesh cheerla
> wrote:
> > This probably means your
> > constraint lengths are too long compared to the domain decomposi
Hi,
Just to note for the users who might read this: the report is valid, some
non-thread-parallel code is the reason and we hope to have a fix for 4.6.0.
For updates, follow the issue #1211.
Cheers,
--
Szilárd
On Wed, Jan 16, 2013 at 4:45 PM, Berk Hess wrote:
>
> The issue I'm referring to
Thank you!
It's a good news!
James
2013/1/17 Carlo Camilloni :
> Hi,
>
> yes I can confirm you that PLUMED will be available for gromacs-4.6!
> We are currently testing it.
>
> Carlo
>
>> Message: 6
>> Date: Wed, 16 Jan 2013 12:54:11 -0500
>> From: Michael Shirts
>> Subject: Re: [gmx-users] met
It should be in the top folder. If you install GROMACS recently and can not
find the .dat just install GROMACS again.
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Devika N T
Sent: Thursday, 17 January 2013 4:34 PM
To: Discuss
Thank you Emanuel
I have followed the path only usr/share/gromacs/top -- but was missing
Then I followed /usr/local/gromacs/share/gromacs/top - I could find
"residuetype.dat "
Previously I was having gromacs version 4.0.7, now I have installed 4.5.5.
So I doubt some problem which removing and in
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