On 7/2/13 8:38 PM, Pavithra wrote:
Dear Sir,
thanks for the reply.
what is the solution for this problem?
can I just increase the box size? if so how?
Use editconf to set a new box size while retaining the coordinates of the
current center. Then add water with genbox.
how to change the s
Dear Sir,
thanks for the reply.
what is the solution for this problem?
can I just increase the box size? if so how?
how to change the size without affecting the pope bilayer?
regards,
pavithra
Message: 4
> Date: Tue, 2 Jul 2013 12:10:37 -0400
> From: Justin Lemkul
> Subject: Re: [gmx-users] prob
Hi Tsjerk,
I have written g_traj -n index.ndx -f traj.trr -s topol.tpr and it works.
Thank you for your prompt reply.
Best,
Silvia
2013/7/2 Tsjerk Wassenaar
> Hi Silvia,
>
> The .xtc file does not contain velocities. You'll need to use the .trr
> file.
>
> Cheers,
>
> Tsjerk
>
>
> On Tue, Jul
Mark,
Upgrading to the latest/greatest cmake (2.8.11.1) fixed the problem in my case.
Thanks,
Malcolm
On Tuesday 02 July 2013 14:20:44 Mark Abraham wrote:
> Following
> http://www.gromacs.org/Documentation/Installation_Instructions#.c2.a7_4.6._Native_GPU_acceleration
> could help. The FindCUDA
Justin answered this question about average structures earlier today.
Please read his answer.
Mark
On Tue, Jul 2, 2013 at 8:37 PM, Shine A wrote:
> Sir,
>
> I trying to calculate ground state conformational ensemble of a
> peptide by comparing experimental chemical shift and predicted chemi
Following
http://www.gromacs.org/Documentation/Installation_Instructions#.c2.a7_4.6._Native_GPU_acceleration
could help. The FindCUDA.cmake in CMake 2.8.1 might not work properly
- we don't test that combination. Trying a newer CMake could help, but
I would avoid 2.8.7, 2.8.9 and 2.8.10 because th
I see the same problem as Justin.
The real problem lies here:
mdrun -nt 4 -v -s 10step.tpr -c nonlinear.gro -e nonlinear.edr -x
nonlinear.xtc -o nonlinear.trr -g nonlinear.log -cpi nonlinear.cpt -cpo
nonlinear.cpt -rdd 2.5
Due to the '-cpi nonlinear.cpt' mdrun thinks the the time now the
end
Hi Sonika,
cmake needs a specification of the path where the source code is. In
addition to that, it is best to build it in a separate directory. As
explained on the website, in your gromacs directory:
mkdir build
cd build
cmake ../
make
make install
Hope it helps,
Tsjerk
On Tue, Jul 2, 2013
All,
I'm attempting to build gromacs 4.6.2 with a bit of everything: CUDA support,
MPI, Intel compilers, etc. using the new cmake system. I've set CC and CXX to
specify the Intel compilers:
[root@login002 build]# echo $CC
icc
[root@login002 build]# echo $CXX
icc
and sourced the setup script
Hi everyone,
I am trying to install Gromacs on OS X and following the installation guide, in
section 4.1, I get an output shown as follows:
Sonikas-MacBook-Pro:Downloads sonikagahlawat$ cd gromacs-4.6.2
Sonikas-MacBook-Pro:gromacs-4.6.2 sonikagahlawat$ cmake
cmake version 2.8.11.1
Usage
cmake
Hi Silvia,
The .xtc file does not contain velocities. You'll need to use the .trr file.
Cheers,
Tsjerk
On Tue, Jul 2, 2013 at 8:25 PM, Silvia wrote:
> Dear users and experts,
> I am new in the list and I am writing because I have a problem to get
> velocities from the trajectory file. When I
Sir,
I trying to calculate ground state conformational ensemble of a
peptide by comparing experimental chemical shift and predicted chemical
shifts.For that I did REMD simulation at 8 temperatures.Then using
g_cluster clustered.Here is it reasonable to compare the chemical shift of
average st
Dear users and experts,
I am new in the list and I am writing because I have a problem to get
velocities from the trajectory file. When I use this command line g_traj -n
index.ndx -s topol.tpr -f traj.xtc -ov, I obtain the veloc.xvg file but
there is no data inside. I have the same problem on the f
So I would have to successively set tinit to the time of the last restart?
Can I ask why that doesn't seem to be a problem when I am simply switching
from saving every 10steps to every 100 steps? I am not at time zero then
either, but at 2ps and grompp and mdrun did not complain then.
Justin Lem
On Tue, Jul 2, 2013 at 1:23 PM, Neha wrote:
> Hi,
>
> So the commands are:
>
> grompp -f 10step.mdp -p dppc_bilayer.top -o 10step.tpr -c dppc_bilayer.gro
>
> mdrun -nt 4 -s 10step.tpr -c nonlinear.gro -e nonlinear.edr -x
> nonlinear.xtc
> -o nonlinear.trr -g nonlinear.log -cpo nonlinear.cpt -rdd
Hi,
So the commands are:
grompp -f 10step.mdp -p dppc_bilayer.top -o 10step.tpr -c dppc_bilayer.gro
mdrun -nt 4 -s 10step.tpr -c nonlinear.gro -e nonlinear.edr -x nonlinear.xtc
-o nonlinear.trr -g nonlinear.log -cpo nonlinear.cpt -rdd 2.5
grompp -f 100step.mdp -c 10step.tpr -p dppc_bilayer.top
On Tue, Jul 2, 2013 at 12:46 PM, Neha wrote:
> So I tried doing this and ran into another problem.
>
> I made two mdp files, one that stored data every ten steps and one every
> hundred steps
>
> I was thinking I would store data like this:
>
> 10
> 20
> 30
> .
> .
> .
> 100
> 200
> .
> .
> .
> 1
So I tried doing this and ran into another problem.
I made two mdp files, one that stored data every ten steps and one every
hundred steps
I was thinking I would store data like this:
10
20
30
.
.
.
100
200
.
.
.
1000
And then I would start another 'block' that would go
1010
1020
.
.
.
1100
On Tue, Jul 2, 2013 at 11:36 AM, Pavithra wrote:
> Dear gromacs users,
>
> I'm new to simulation.
> I'm running a membrane protein simulation with gromacs and am following
> KALP tutorial.
> I skipped inflategro and used g_membed command to insert my protein complex
> into POPE membrane.
> I foll
Please keep all discussions on the mailing list. Others following the
thread may be interested in it. The paper that came immediately to mind
was dx.doi.org/10.1016/j.bpj.2010.04.062.
-Justin
On Tue, Jul 2, 2013 at 11:43 AM, wrote:
> Hi,
>
> Sorry for use the email, I am new in the list and I
Dear gromacs users,
I'm new to simulation.
I'm running a membrane protein simulation with gromacs and am following
KALP tutorial.
I skipped inflategro and used g_membed command to insert my protein complex
into POPE membrane.
I followed the tutorial and got the work done but with a peculiar error.
On Tue, Jul 2, 2013 at 10:51 AM, Melchor S. wrote:
> Hi Tsjerk,
>
> I read the sae that you say about the PME and the twin cutoff, but as I
> have seen that a lot of studies in that people use Gromos with PME and a
> Vander Vaals cutoff so small as mine, I didn't change it, for mantain the
> sam
Hi Tsjerk,
I read the sae that you say about the PME and the twin cutoff, but as I
have seen that a lot of studies in that people use Gromos with PME and a
Vander Vaals cutoff so small as mine, I didn't change it, for mantain the
same settongs than in OPLS simulations.
About the structures are v
On 02/07/13 12:10, Justin Lemkul wrote:
On Tue, Jul 2, 2013 at 5:30 AM, Richard Broadbent <
richard.broadben...@imperial.ac.uk> wrote:
Not sure exactly what merging together means, for visualisation I
generally use vmd as this supports gromacs files directly.
If I understand correctly (and
Hi Melchor,
Have you looked at the structures? The GROMOS people suggest using
twin-range cut-off with reaction field correction, and the Vanderwaals
cutoff you use seems a bit small, as 1.4 nm is commonly used with GROMOS.
Maybe that makes a difference.
Cheers,
Tsjerk
On Tue, Jul 2, 2013 at 3
I expected to see how the RMSD increases with time respect the closed
cristallographic structure and decreases with time respect to the open
crystal structure.
I obtained it for OPLS, but with gromos I obtain a kind of mixture in that
you see that the structure behaves different between the open a
Hi Melchor,
So what did you expect, what did you do, and what did you get?
Cheers,
Tsjerk
On Tue, Jul 2, 2013 at 2:45 PM, Melchor S. wrote:
> Hi all,
>
> I am trying to calculate an RMSD of two simulations. All the setting are
> equal for both, but i use OPLS in one and for the other gromos
Possibly. There were appending bugs fixed during the 4.5.x series.
There are also bugs in file systems that prevent appending working
properly in all cases. Check out the release notes, consider updating,
or using -noappend.
Mark
On Tue, Jul 2, 2013 at 2:41 PM, Humphrey Morhenn
wrote:
> On 07/02
Hi all,
I am trying to calculate an RMSD of two simulations. All the setting are
equal for both, but i use OPLS in one and for the other gromos53a6.
I wanted to calculate the RMSD between the trajectory and the
crystallographic structures(Open and closed forms). The simulation involves
a protein
On 07/02/2013 01:34 PM, Justin Lemkul wrote:
> On Tue, Jul 2, 2013 at 7:26 AM, Humphrey Morhenn <
> humphrey.morh...@frm2.tum.de> wrote:
>
>> Dear users,
>>
>> there seem to be alot of frames missing in my .trr trajectory file and I
>> wonder if anyone knows how to recover the (hopefully not lost)
On Tue, Jul 2, 2013 at 7:26 AM, Humphrey Morhenn <
humphrey.morh...@frm2.tum.de> wrote:
> Dear users,
>
> there seem to be alot of frames missing in my .trr trajectory file and I
> wonder if anyone knows how to recover the (hopefully not lost) information.
>
> tinit= 0
> dt
Dear users,
there seem to be alot of frames missing in my .trr trajectory file and I
wonder if anyone knows how to recover the (hopefully not lost) information.
tinit= 0
dt = 0.001
nsteps = 12000
nstxout = 100
W
On Tue, Jul 2, 2013 at 5:30 AM, Richard Broadbent <
richard.broadben...@imperial.ac.uk> wrote:
> Not sure exactly what merging together means, for visualisation I
> generally use vmd as this supports gromacs files directly.
>
>
If I understand correctly (and the OP can clarify if I haven't), it so
It's just the xvv file. g_wham uses the letter 'z' to denote the reaction
coordinate.
Erik
On 2 Jul 2013, at 11:32, battis...@libero.it wrote:
>
>
>
>
>
>
> Dear users and experts
>
> I'm doing an umbrella-samplig calculation to obtain the PMF when two
> structure (A and B) are at vario
Dear users and experts
I'm doing an umbrella-samplig calculation to obtain the PMF when two structure
(A and B) are at various X distances.
I setted my md-umbrella.mdp file as in follows:
; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull = umbr
Dear users and experts
I'm doing an umbrella-samplig calculation to obtain the PMF when two structure
(A and B) are at various X distances.
I setted my md-umbrella.mdp file as in follows:
; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull = umbrella
Not sure exactly what merging together means, for visualisation I
generally use vmd as this supports gromacs files directly.
Your problem might be to do with, using rlist, rcoulomb, and rvdw set to
0 is not the standard way to do an infinite cut-off normally you set
them to -1 as in the manual
Sir,
I did a 10 ns REMD simulation for a peptide, 8 replicas using amber
force field.Then extracted pdb file from the trajectory and clustered using
g_cluster. The I viewed the average structure of the cluster in pymol .But
here the atoms are merged togather.why it happends?Is there any pro
Hi Richa,
>From your explanation, I understand you want to know the sum of distances
between each frame and its corresponding filtered frame. I think it makes
more sense to sum squared distances, but that's a minor detail.
The (non-mass-weighted) RMSD between two structures, written as positional
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