Dear GMX users:
While I am installing gmx4.5.5, an error occured after "make" command :
cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
-funroll-all-loops -std=gnu99 -pthread -I./include -o .libs/grompp grompp.o
-L/home/hzj1000/software/fftw/lib ./.libs/libgmxpreprocess.s
Hi, everyone:
when I compiled GMX4.5.5, I encountered a problem and failed many times， SOS!
Below is my config.log:
/usr/bin/uname -p = unknown
/bin/uname -X = unknown
/bin/arch = x86_64
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo =
Dear Everyone,
I am Saurav B. Saha from India. I am newbie to gromacs. I am interested in
using gromacs for ligand receptor interaction. But when i started my first step
by using "pdb2gmx -f structure.pdb -water tip3p" i am getting fatal error
(Fatal error:Atom CD not found in residue seq.nr. 7
Dear users,
I was trying to simulate a protein dimer covalently bond with
a disulphide bond (230+230 aa long). I used usual protocol
as used for simulation of a monomeric protein, using gromacs-
4.5.3, dodecahedron box, tip4p water model and protein to
box distance of 1 (-d in editconf). In the mi
Hi,
Thanks for this - very helpful and I think I've been able to identify the
structures I'm interested in.
Incidentally, I saw the earlier correspondence about plotting the axes using
g_sham.
I'm having similar difficulties - I can generate axes, based on the data range
using -xmax and -xmin
Saurav Saha wrote:
Dear Everyone,
I am Saurav B. Saha from India. I am newbie to gromacs. I am interested in using gromacs
for ligand receptor interaction. But when i started my first step by using "pdb2gmx
-f structure.pdb -water tip3p" i am getting fatal error (Fatal error:Atom CD not
fou
Parul tew wrote:
Thanks for the reply Justin,
> In theory, that should work. Please post the entirety of your
.mdp file.
Have you done any prior equilibration, or have you moved straight into
annealing? I would suggest a restrained NVT before applying NPT or
annealin
Kavyashree M wrote:
Dear users,
I was trying to simulate a protein dimer covalently bond with
a disulphide bond (230+230 aa long). I used usual protocol
as used for simulation of a monomeric protein, using gromacs-
4.5.3, dodecahedron box, tip4p water model and protein to
box distance of 1 (-d
Thanks.
On Wed, Sep 21, 2011 at 5:07 PM, Justin A. Lemkul wrote:
>
>
> Kavyashree M wrote:
>
>> Dear users,
>>
>> I was trying to simulate a protein dimer covalently bond with
>> a disulphide bond (230+230 aa long). I used usual protocol
>> as used for simulation of a monomeric protein, using gr
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Dear Gromacs community,
A new maintenance release of Gromacs is available for download at
ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz.
Some notable updates in this release:
* Improved pdb2gmx -chainsep option and reintroduced the -merge option.
* Fixed mdrun file appending trunca
Dear Gromacs Users,
>
>
>
>I want to simulate 150 surfactant molecules in the water by MARTINI
>Coarse-Grained force field, and I have several questions please:
>1- I defined 2 groups in index.ndx file named "surfactants"
and "w_ion_ wf" that second group is consist of water,
a
Dear Gromacs Users,
>
>
>
>I want to simulate 150 surfactant molecules in the water by MARTINI
>Coarse-Grained force field, and I have several questions please:
>1- I defined 2 groups in index.ndx file named "surfactants"
and "w_ion_ wf" that second group is consist of water,
a
Hi,
for your entertainment and as a reach-out to younger scientists GROMACS
is now on Facebook. Please look us up at:
http://www.facebook.com/pages/GROMACS/257453660934850
We're looking forward to your comments.
Cheers,
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Mole
Dear gmx users,
Does someone know how to deal with the error mesage bellow ?
With my best regards,
Tanos C. C. Franca.
Program mdrun, VERSION 4.5.4
Source code file: domdec_con.c, line: 693
Fatal error:
DD cell 2 1 0 could only obtain 273 of the 275 atoms that are connected
via constraints from
Tanos Franca wrote:
Dear gmx users,
Does someone know how to deal with the error mesage bellow ?
The DD geometry depends upon the configuration of the system, constraints
applied, cutoffs, and any other special restraints (like distance restraints)
that may be present. The error message su
Hi everybody,
I have a small question. I read somewhere that for a better performance on
coupling the Temperature of a system is better do it by dividing the system in
groups, let say protein and solvent, and coupling them to the same target
temperature. Is it remaining true for other integrato
On 22/09/2011 1:22 AM, Marcelino Arciniega Castro wrote:
Hi everybody,
I have a small question. I read somewhere that for a better performance on
coupling the Temperature of a system is better do it by dividing the system in
groups, let say protein and solvent, and coupling them to the same ta
Cool... :-)
> Hi,
>
> for your entertainment and as a reach-out to younger scientists GROMACS
> is now on Facebook. Please look us up at:
>
> http://www.facebook.com/pages/GROMACS/257453660934850
>
> We're looking forward to your comments.
>
> Cheers,
> --
> David van der Spoel, Ph.D., Professor o
Dear users,
g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res
With the option -od the root mean square deviation with respect to the
reference structure is calculated.
Then,
RMSDEV is the RMSD per residue (the root mean square deviation with respect
to the reference structure is calcul
ahmet yıldırım wrote:
Dear users,
g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res
With the option -od the root mean square deviation with respect to the
reference structure is calculated.
Then,
RMSDEV is the RMSD per residue (the root mean square deviation with
respect to the
Dear Gromacs Users,
>
>
>
>I want to simulate 150 surfactant molecules in the water by MARTINI
>Coarse-Grained force field, and I have several questions please:
>1- I defined 2 groups in index.ndx file named "surfactants"
and "w_ion_ wf" that second group is consist of water,
a
Dear users,
1.) During the simulation the mean potential energy is minus (-) value. What
does this mean? Why minus?
2.) let's say, Interface/Buried Surace Area (ISA) between protein and ligand
was calculated and hydrophobic ISA obtained greater than hydrophilic ISA.
What does this mean?
No one is
Hi,
The sd integrator is described in the manual as follows:
sd
An accurate leap-frog stochastic dynamics integrator. Four Gaussian
random number are required per integration step per degree of freedom.
With constraints, coordinates needs to be constrained twice per
integration step. Depending on
ahmet yıldırım wrote:
Dear users,
1.) During the simulation the mean potential energy is minus (-) value.
What does this mean? Why minus?
Net attraction.
2.) let's say, Interface/Buried Surace Area (ISA) between protein and
ligand was calculated and hydrophobic ISA obtained greater than
Hi,
I don't know if my question somehow got lost, or if I forgot to provide
some necessary information. Anyway it would be of great help to me, if
someone could tell me her/his opinion on the problem. I need to use
particle decomposition as I want to introduce distance restraints from
2-6nm, which
On 22/09/2011 6:21 AM, Sai Pooja wrote:
Hi,
The sd integrator is described in the manual as follows:
sd
An accurate leap-frog stochastic dynamics integrator. Four Gaussian
random number are required per integration step per degree of freedom.
With constraints, coordinates needs to be constrained
But is the effect of varying ld_seed.. can that make different
trajectories stochastic?
On Wed, Sep 21, 2011 at 7:40 PM, Mark Abraham wrote:
> On 22/09/2011 6:21 AM, Sai Pooja wrote:
>>
>> Hi,
>>
>> The sd integrator is described in the manual as follows:
>> sd
>> An accurate leap-frog stochast
On 22/09/2011 9:57 AM, Sai Pooja wrote:
But is the effect of varying ld_seed.. can that make different
trajectories stochastic?
Any single MD or SD trajectory is literally stochastic. Either can start
from the same point with respectively different ld_seed or gen_seed and
diverge.
Mark
O
On 22/09/2011 8:45 AM, Florian Altvater wrote:
Hi,
I don't know if my question somehow got lost, or if I forgot to provide
some necessary information. Anyway it would be of great help to me, if
someone could tell me her/his opinion on the problem. I need to use
particle decomposition as I want to
On 21/09/2011 7:59 PM, Jinan Niu wrote:
Hi, everyone:
when I compiled GMX4.5.5, I encountered a problem and failed many
times, SOS!
Below is my config.log:
More useful would be the information that you've been following the
online installation guide, and what your configure line was. As it
On 21/09/2011 7:27 PM, zhongjin wrote:
Dear GMX users:
While I am installing gmx4.5.5, an error occured after "make" command :
cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
-msse2 -funroll-all-loops -std=gnu99 -pthread -I./include -o
.libs/grompp grompp.o -L/home/hzj1000/sof
On 20/09/2011 9:06 AM, César Ávila wrote:
Dear all,
I am running REMD simulations in gromacs. Taking advantage of vsites I
have set the timestep to 5 fs. In the mdp file I have adjusted the
energy and frames to be written every 1000 steps (5 ps). While running
the simulations I have also selec
On Wed, Sep 21, 2011 at 9:01 PM, Mark Abraham wrote:
> On 21/09/2011 7:27 PM, zhongjin wrote:
>
> Dear GMX users:
> While I am installing gmx4.5.5, an error occured after "make" command :
> cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
> -funroll-all-loops -std=gnu99 -
Dear All
I'd like to perfom a MD simulation on a membrane protein using DLPC or DPPC
system
I've downloaded the API package from this link
http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies
DPPC.zip and DLPC.zip by schiu
How can I use them? Where can I get a tutorial or comm
Dear All
I'd like to perfom a MD simulation on a membrane protein using DLPC or DPPC
system
I've downloaded the API package from this link
http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies
DPPC.zip and DLPC.zip by schiu
How can I use them? Where can I get a tutorial or comm
On Thu, Sep 22, 2011 at 11:34 AM, elisa carli wrote:
> Dear All
>
> I'd like to perfom a MD simulation on a membrane protein using DLPC or DPPC
> system
> I've downloaded the API package from this link
> http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies
>
> DPPC.zip and DLPC.
Hi users,
The g_mindist gives the minimum distance between the atoms other than the
actual distance.
Thanks
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Hi Aiswarya,
What did you do, what did you get, what did you expect and what is
your hunch regarding the difference between your result and your
expectation?
Tsjerk
On Thu, Sep 22, 2011 at 8:21 AM, aiswarya pawar
wrote:
> Hi users,
>
> The g_mindist gives the minimum distance between the atoms
On 22/09/2011 4:43 PM, Tsjerk Wassenaar wrote:
Hi Aiswarya,
What did you do, what did you get, what did you expect and what is
your hunch regarding the difference between your result and your
expectation?
And have you checked out g_mindist -h?
Mark
Tsjerk
On Thu, Sep 22, 2011 at 8:21 AM,
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