As the consequence I've done my NMA calculations without of any constraints
:)
integrator= nm; Normal Mode Analysis
constraints = none
but I'm not sure if this could be valid because I didnt found any literature
of such NMA in Gromacs. Could someone provide me with the appro
Hi all. I need your advices about my task which is closely associated with
ATP toplogy in the binding site. As I understood from one of the letters (
http://archive.ambermd.org/201106/0522.html) I can use antechamber or derive
charges from the site linked in the letter. But the ATP's phosphate tail
On 24/10/2011 3:12 AM, James Starlight wrote:
I want to come back to the question of the NMA in the Gromacs :)
I've found in manual possible algorithms of this analysis- I must
calculate Hessian matrix via Md-run and then calculate modes with
g_nmens program
1- I've performed CG minimizati
On 24/10/2011 6:56 PM, James Starlight wrote:
As the consequence I've done my NMA calculations without of any
constraints :)
integrator= nm; Normal Mode Analysis
constraints = none
but I'm not sure if this could be valid because I didnt found any
literature of such NMA i
Dear Gmx Users,
I am trying to convert my trajectory using trjconv. My system is made of 10
ligands and protein. Protein is jumping
divided into parts. The same is with my ligands. I am confused about the
point 2 and 3:
2. Extract the first frame from the trajectory as reference for removing
j
Steven Neumann wrote:
Dear Gmx Users,
I am trying to convert my trajectory using trjconv. My system is made
of 10 ligands and protein. Protein is jumping
divided into parts. The same is with my ligands. I am confused about the
point 2 and 3:
2. Extract the first frame from the trajec
Hi,
You don't need a .tpr file for removing jumps; a pdb/gro file will do.
Cheers,
Tsjerk
On Oct 24, 2011 2:51 PM, "Justin A. Lemkul" wrote:
Steven Neumann wrote: > > Dear Gmx Users, > I am trying to convert my
trajectory using trjconv. ...
trjconv -dump 0
> > 3. Remove jumps if you want t
Sorry guys but I do not get this...
I used:
1. First make your molecules whole if you want them whole
trjconv -f md2.trr -s md2.tpr -pbc whole -o md2whole.xtc (I have chosen my
whole system for input and output)
2. I do not need cluster anything
3. Extract the first frame from the traject
Hi Steven,
Output can also be .pdb or .gro
Cheers,
Tsjerk
On Oct 24, 2011 3:59 PM, "Steven Neumann" wrote:
Sorry guys but I do not get this...
I used:
1. First make your molecules whole if you want them whole
trjconv -f md2.trr -s md2.tpr -pbc whole -o md2whole.xtc (I have chosen my
who
Thank you both!!!
Steven
On Mon, Oct 24, 2011 at 3:01 PM, Tsjerk Wassenaar wrote:
> Hi Steven,
>
> Output can also be .pdb or .gro
>
> Cheers,
>
> Tsjerk
>
> On Oct 24, 2011 3:59 PM, "Steven Neumann" wrote:
>
> Sorry guys but I do not get this...
>
>
> I used:
>
> 1. First make your molecules
Dear Gromacs users,
I am trying to install gromacs on my cluster using Intel Compiler 11.1.072 and
FFTW3. But I met the following error message
icc -DHAVE_CONFIG_H -I. -I../../../src -I/usr/include/libxml2
-I../../../include -I/usr/local/include -xHOST
-I/home/users/ymei/software/fftw3/intel/i
I am interesting in modeling a small molecule ligand-protein complex that
involves a cationic ligand encapsulated by several aromatic residues that form
a box around the cation. However, md simulations result in the cation moving
outside the box. I am using the CHARMM27 forcefield. Is there a wa
Last question:
I would like to visualise my whole trjajectory looking at one of the ligands
only which stacked to the loop of my protein. Which option of trjconv will
be suitable to see whole trajectory of this ligand withoout any shifts on
the screen so I will be able to produce a movie? I assume
EGY wrote:
I am interesting in modeling a small molecule ligand-protein complex that
involves a cationic ligand encapsulated by several aromatic residues that form
a box around the cation. However, md simulations result in the cation moving
outside the box. I am using the CHARMM27 forcefield
Steven Neumann wrote:
Last question:
I would like to visualise my whole trjajectory looking at one of the
ligands only which stacked to the loop of my protein. Which option of
trjconv will be suitable to see whole trajectory of this ligand withoout
any shifts on the screen so I will be abl
Justin, hello!
I have forced with some problem during final stage of your turorial.
I dont know why but after NPT phase my sytem has occured in the standart
cubic box instead of dodecahedron (after all previosly phases my system was
in correct box).
So when I've passed my system in the MD stage
I understand this but I've not been able found such information. I dont need
in the most accurately parametries for all cutt-offs of my system but I
want to gain inside into the basic cutt- offs worked with the Normal mode
analysis.
E.g I've found that PME is not worked here. So I must to constra
Thanks for taking the time to answer, but I think my wording may have confused
my question. I shouldn't have used the word box. Within the protein their are
several aromatic residues that interact with the small molecule cation. I would
like to preserve these interactions throughout the simulati
James Starlight wrote:
Justin, hello!
I have forced with some problem during final stage of your turorial.
I dont know why but after NPT phase my sytem has occured in the standart
cubic box instead of dodecahedron (after all previosly phases my system
was in correct box).
So when I've pa
EGY wrote:
Thanks for taking the time to answer, but I think my wording may have confused my
question. I shouldn't have used the word box. Within the protein their are several
aromatic residues that interact with the small molecule cation. I would like to preserve
these interactions througho
Justin,
I've used trjconv -pbc mol -ur compact
but the final picture was still wrong :(
So I think that something happened with my box because
1- If the cubic representation is set on default why other .gro structures
were visualized in VMD in dodecahedral box on default ?
2- Why the pereodic
Hi,
The error messages are all referring to SSE 4.1 packed integer min/max
operations not being recognized. I assume that these were enabled by
the "-xHOST" compiler option, and icc automatically generated these
instructions - the files it's complaining about are even temporary
files.
Could it be
Hi Matt,
Yes, you should use the "force-device=yes" option, the patch which was
meant to update the list of compatible GPUs didn't make it for 4.5.5.
Cheers,
--
Szilárd
On Sun, Oct 23, 2011 at 10:24 PM, Matt Larson wrote:
> I am having an error trying to use a compiled mdrun-gpu on my GPU set
James Starlight wrote:
Justin,
I've used trjconv -pbc mol -ur compact
but the final picture was still wrong :(
So I think that something happened with my box because
1- If the cubic representation is set on default why other .gro
structures were visualized in VMD in dodecahedral box on d
Please keep all discussions on the mailing list! Also, I'm also CC-ing
to the gmx-devel list, maybe somebody over there has an better what
causes your CMake issue.
>>> //Flags used by the compiler during all build types
>>> CMAKE_C_FLAGS:STRING=' -msse2 -ip -funroll-all-loops -std=gnu99 '
>>>
>>>
I've just realized that both you and the similar report you linked to
were using CMake 2.8.3. If you don't succeed could you try another
CMake version?
--
Szilárd
On Mon, Oct 24, 2011 at 11:14 PM, Szilárd Páll wrote:
> Please keep all discussions on the mailing list! Also, I'm also CC-ing
> to
Hi all,
I am using GROMACS with the plugin PLUMED in double precision. The
speed has gone down by a huge margin and I was wondering if there is
something in 1) compilation 2) md parameters that could be
contributing to this?
md parameters:
title= NVT simulation (constant num
Szilárd,
Thanks- gromacs 4.5.5 is working with my NVidia card with the "force
option". I found one weirdness - if I check the card temperature
(using NVIDIA's configuration tool in X11) it seems like this messes
up the MR and all the trajectories after that point have no atoms in
VMD. So, that'
On 25/10/2011 3:30 AM, James Starlight wrote:
I understand this but I've not been able found such information. I
dont need in the most accurately parametries for all cutt-offs of my
system but I want to gain inside into the basic cutt- offs worked with
the Normal mode analysis.
The cut-offs
On 25/10/2011 9:54 AM, Sai Pooja wrote:
Hi all,
I am using GROMACS with the plugin PLUMED in double precision. The
speed has gone down by a huge margin and I was wondering if there is
something in 1) compilation 2) md parameters that could be
contributing to this?
Simply moving to double preci
On 25/10/2011 4:20 AM, EGY wrote:
Thanks for taking the time to answer, but I think my wording may have confused my
question. I shouldn't have used the word box. Within the protein their are several
aromatic residues that interact with the small molecule cation. I would like to preserve
these
Dear Szilárd，
Thank you very much. I removed -xHOST from CFLAGS and FFLAGS, and now it runs
correctly.
As for Intel Compile 2011 sp1 + openmpi on my cluster, mpif90 and mpicc give
"segmentation fault" error message.
Best regards,
Ye
2011-10-25
From： Szil醨d P醠l
Date： 2011-10-25 03:42:1
Thank you so much Mark. You are right about the cut-off values. I am
now using 1.2nm which appears more commonly in literature. If possible
please take a look at these statistics:
R E A L C Y C L E A N D T I M E A C C O U N T I N G
Computing: Nodes Number G-Cycles
On 25/10/2011 3:11 PM, Sai Pooja wrote:
Thank you so much Mark. You are right about the cut-off values. I am
now using 1.2nm which appears more commonly in literature. If possible
please take a look at these statistics:
R E A L C Y C L E A N D T I M E A C C O U N T I N G
Computi
This was due to that in .gro file corresponded to the end of productive MD
I've found this http://i1209.photobucket.com/albums/cc394/own11/mdL.png
It's looks like the protein moved out from box so I've thought that some
error occured during stimulation
>>
> I don't understand this statement. You
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