Thanks Justin!
On 10/17/11, Justin A. Lemkul wrote:
>
>
> Tom wrote:
>> Justin
>>
>> you have good experience of pulling.
>>
>> If you have time, please help with this publling problem:
>> abrupt change in sign of 1dZ on output file: pullx.xvg. Thanks a lot!
>>
>
> I already commented:
>
> http:/
On Sat, Oct 29, 2011 at 12:51 AM, Victor wrote:
> Hello gmx-users
>
> I have compiled gromacs on Debian/Linux wiht the option --with-x but the
> ngmx binary has not been generated. I don´t have gnome or kde installed, but
> I have installed xserver-xorg and I can export VMD with ssh.
> Do I need
Dear all,
I am trying to calculate interfacial tension between Xylene/CHCl3 mixture
and water. I have created a box (5*5*15) with a water layer in the middle.
I run NVT for 200ps to stabilize the temperature (298 K). After that I run
NPT equilibration for ref_p =1 bar with Berendsen isotropic pres
I've been having problems getting implicit solvent systems (which are
probably fairly experiment still in gromacs) to work correctly. I've
been modelling a protein of about 11000 atoms with hydrogens in a 2 ns
simulation. By the end of the simulation, the temperature has risen
from 300 K to 496 K
Hello Ahmet:
The warnings originating from the LINCS algorithm are dee to either
incorrect topology (TOP file) of certain particle or bad initial
configuration (GRO file).
If you don't provide this information about your problematic system,
there is no chance to help you.
--
Dr. Vitaly V. Chaba
Dear Gromacs Users!
I wounder to know about possible algorithm of preparation of the existing
lipid bilayer for further simulation.
E.g I have some pre-equilibrated bilayer consisted of symmetrical lipid
organization. Now I'd like to remove some lipids from the edges of my
bilayer to reduce overal
Dear Gromacs Users,
I have a question about how to ouput the force between two groups.
Suppose the system consists of the groups: A, B, C and D.
I need the force only between the groups A and B.
g_traj looks only to be able to report the overal forces and cann not distiguish
the forces from diff
On Mon, Oct 31, 2011 at 9:28 AM, Sanku M wrote:
> Hi,
> I just compiled gromacs 4.5.4 in a cluster. But, I find that if I try to
> make use of threading introduced in gromacs 4.5.x series, it does not work.
> After issuing command like mdrun -v -s , I expected that for my 8-core
> processor whic
On 31/10/2011 4:05 AM, Tom wrote:
Dear Gromacs Users,
I have a question about how to ouput the force between two groups.
Suppose the system consists of the groups: A, B, C and D.
I need the force only between the groups A and B.
g_traj looks only to be able to report the overal forces and cann
Greeting
i'm doing a MD simulation for a monomeric protein over 10 ns, my
question is :
* for my MD how do i know that it has equilibrated and suitable for
study ?,is it RMSD , Radius of gyration and potential energy stability
enough ? OR should i look for other parameters and do multiple
si
Hello all,
I am using amber99SB to model an antibody with organic ligands.
I know we could choose to restrain all atoms or only heavy atoms during the
equilibration. But I wonder if this really matters for my system. As far as
I know, equilibration is aimed at getting the temperature and pressure
Mark, hello!
I think that there is some error durins saving of my minimization data
As the result of the minimization I've obtained
(1)
Low-Memory BFGS Minimizer converged to machine precision in 3723 steps,
but did not reach the requested Fmax < 0.
Potential Energy = 2.08789280994511e+03
Maxi
On 24.10.2011 23:23, Szilárd Páll wrote:
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?
I could replicate the error with the simple cmake inviocation you proposed in
your reply:
cmake ../
Hi
There has been a number of reports lately about ill-behaving simulations using
implicit solvent. I'm currently trying to investigate the cause of this, as
such simulations used to work very nice in our hands.
In the meantime I would advice to use implicit solvent with caution.
Thanks
/Per
Dear Gromacs Users!
I'd like to know about external software wich could be used for structure
processing for the futher simulation in Gromacs. Today I've tried one of the
most popular such software Amber tools but I've forced with problems during
compilation of it ") So I'm looking for possible a
James Starlight wrote:
Mark, hello!
I think that there is some error durins saving of my minimization data
As the result of the minimization I've obtained
(1)
Low-Memory BFGS Minimizer converged to machine precision in 3723 steps,
but did not reach the requested Fmax < 0.
Potential Energy =
I would also add that the settings provided below probably produce severe cutoff
artifacts. In my experience, the only stable settings are those of the
all-vs-all kernel (with infinite cutoffs).
-Justin
Per Larsson wrote:
Hi
There has been a number of reports lately about ill-behaving sim
Dear Gmx Users,
My system consists of 10 ligands and protein. I am calculating the hydrogen
bonds between each residue and my ligands (LIG). The overall charge of each
ligand is zero.
I used:
g_hbond -f md2.trr -s md2.tpr -n SystemGRP.ndx -num
RESIDUEwithLigandsHbond.xvg
And I found one residue
On 31/10/2011 7:39 PM, larifsofiene wrote:
Greeting
i'm doing a MD simulation for a monomeric protein over 10 ns, my
question is :
* for my MD how do i know that it has equilibrated and suitable for
study ?,is it RMSD , Radius of gyration and potential energy stability
enough ? OR should i l
On 31/10/2011 10:19 PM, Steven Neumann wrote:
Dear Gmx Users,
My system consists of 10 ligands and protein. I am calculating the
hydrogen bonds between each residue and my ligands (LIG). The overall
charge of each ligand is zero.
I used:
g_hbond -f md2.trr -s md2.tpr -n SystemGRP.ndx -num
RES
On 31/10/2011 3:36 PM, lina wrote:
On Mon, Oct 31, 2011 at 9:28 AM, Sanku M wrote:
Hi,
I just compiled gromacs 4.5.4 in a cluster. But, I find that if I try to
make use of threading introduced in gromacs 4.5.x series, it does not work.
After issuing command like mdrun -v -s , I expected tha
Dear Users,
I was trying to run a simulation (gromacs4.5.3)
on a Bluegene/L machine. But I was unable to run.
System admin say that I need to change the input
file. I am not sure what needs to be changed in the
input file which specifies no. of nodes usage.
I am not familiar with the bluegene mac
ahmet yıldırım:
If you want a personal mentoria, you will need to pay for it first. If
you strive to get a FREE help, all correspondence should be kept in
the mailing list to save up an archive for other gromacs users.
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochest
You should provide topology file, I do NOT need your MDP files.
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
2011/10/31 ahmet yıldırım :
> Dear Dr. Chaban,
>
> Firstly, thanks for your reply. I send you th
On 30/10/2011 8:56 AM, Mirco Wahab wrote:
On 24.10.2011 23:23, Szilárd Páll wrote:
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?
I could replicate the error with the simple cmake inviocati
On 30/10/2011 11:04 AM, Yun Shi wrote:
Hello all,
I am using amber99SB to model an antibody with organic ligands.
I know we could choose to restrain all atoms or only heavy atoms
during the equilibration. But I wonder if this really matters for my
system. As far as I know, equilibration is ai
Dear Gromacs Users!
I could not find how I can add missing hydrogens after their removing by
pdb2gmx -ignh.
I have modified structure of my protein after editing by some soft and I
removed all hydrogens but now I want to add it back in accordance with
gromos ff topology
How I can do it ?
James
> Dear Gromacs Users!
>
>
> I'd like to know about external software wich could be used for structure
> processing for the futher simulation in Gromacs. Today I've tried one of the
> most popular such software Amber tools but I've forced with problems during
> compilation of it ") So I'm looking fo
Kavyashree M wrote:
Dear Users,
I was trying to run a simulation (gromacs4.5.3)
on a Bluegene/L machine. But I was unable to run.
System admin say that I need to change the input
file. I am not sure what needs to be changed in the
input file which specifies no. of nodes usage.
Sounds like y
James Starlight wrote:
Dear Gromacs Users!
I could not find how I can add missing hydrogens after their removing by
pdb2gmx -ignh.
I have modified structure of my protein after editing by some soft and I
removed all hydrogens but now I want to add it back in accordance with
gromos ff topo
Its very unclear for me because after pdb2gmx -f 1.pdb -o conf.gro -ignh
with gromos force field
I've checked conf.gro by VMD and this structure didnt contains any
hydrogens ;o
James
2011/10/31 Justin A. Lemkul
>
>
> James Starlight wrote:
>
>> Dear Gromacs Users!
>>
>> I could not find how I
James Starlight wrote:
Its very unclear for me because after pdb2gmx -f 1.pdb -o conf.gro
-ignh with gromos force field
I've checked conf.gro by VMD and this structure didnt contains any
hydrogens ;o
I highly doubt that. I've used one of the Gromos96 force fields for nearly all
of my
Hello,
System Admin said that the Job fails on 32 and 128 because memory
is insufficient for each task, so upon increasing the nodes, data gets
distributed across more number of nodes and each node gets less
memory occupancy and he also mentioned that he was able to run
on 512 nodes but it was giv
On 31/10/2011 11:29 PM, Kavyashree M wrote:
Hello,
System Admin said that the Job fails on 32 and 128 because memory
is insufficient for each task, so upon increasing the nodes, data gets
distributed across more number of nodes and each node gets less
memory occupancy and he also mentioned that
Dear James:
Next time, please specify exactly what you did in enough detail for
somebody else to reproduce it, much as in a manuscript. e.g. there is
no "dmpc.gro" in that website. I can guess what you did, but that is
not ideal.
I took a look at the files that I suppose you used and the
exactly
all hydrogens were represented as a part of the groupd in wich they were.
So is there possible way to explicit it?
Another question about pdb2gmx. about -term
as I understood this must be used only if atoms for CAP groups are
presented in the PDB file mustnt it?
So what term exactly do? D
James Starlight wrote:
exactly
all hydrogens were represented as a part of the groupd in wich they
were. So is there possible way to explicit it?
I'm not quite sure I follow. A united atom force field, by definition, does not
have aliphatic hydrogens. I suggest you consult the literatu
So does anobody know possible sollution for the reduce size of the existing
bilayer?
E.g I've preequilibrated 128 lipids in bilayer and want to obtain 32 lipid
bilayer and dont perturb overall topology of the system
In my lab there is only extremely weak CPU. it could not make md for large
systems
In some papers I found Gromacs graphs showed indirectly measurements of the
time evolution of the Area per lipid value. What gromac's program could be
used for it for cheacking the above value during simulation runs ?
JAmes
2011/10/29 James Starlight
> It's appeared new question about G_membed
Hi, all!
I am trying to simulate a system of peptide, water, NaCl and DMSO.
I used pdb2gmx to generate .top file for DMSO and then created this .itp:
(initial DMSO structure had been minimized before it was used for box
generation)
[ moleculetype ]
; Namenrexcl
DMSO 3
[
James Starlight wrote:
In some papers I found Gromacs graphs showed indirectly measurements of
the time evolution of the Area per lipid value. What gromac's program
could be used for it for cheacking the above value during simulation runs ?
There is no Gromacs tool for this. For a simpl
Yuri Garmay wrote:
Hi, all!
I am trying to simulate a system of peptide, water, NaCl and DMSO.
I used pdb2gmx to generate .top file for DMSO and then created this .itp:
(initial DMSO structure had been minimized before it was used for box
generation)
[ moleculetype ]
; Namenrexc
Hi Tsjerk,
Thanks for your earlier reply. It makes things clear.
Is it possible that the cosine content of first PC is high because of the
fluctuations in the long loop regions which dominate and not in the
secondary structures. The fluctuations in the loop regions is of no
interest to me and I
Hi,
I have done some steered MD simulation and I want to construct the potential
of mean force from these pull-profile using Jarzinsky's inequality. I wanted to
see whether, in updated version of gromacs, there is any implementation of
extracting PMF from SMD simulations.
If not, can anyone
Thanks, Justin
I'll test your program soon.
Today also I have some problems with generation of the posre for lipids
I have lipid bilayer in pdb. Then I selected one lipid molecule and move it
to separate pdb and convert it to gro via editconf.
Than I've used genres and generate posre file for 1
James Starlight wrote:
Thanks, Justin
I'll test your program soon.
Today also I have some problems with generation of the posre for lipids
I have lipid bilayer in pdb. Then I selected one lipid molecule and move
it to separate pdb and convert it to gro via editconf.
Than I've used genres an
I've done all of that
i have "posre_lipid.itp" - for 1 lipid ( posres for each of 50 atoms )
I've included this in the topology of the bilayer
; Include chain topologies
#include "gromos53a6_lipid.ff/forcefield.itp"
#include "dppc.itp"
; Include water topology
#include "gromos53a6_lipid.ff/spc.
There is a way to extract the PMF from sMD simulations using the
weighted histogram analysis method (WHAM) in gromacs- Justin Lemkul's
tutorial does a nice job of explaining it:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html
- Laura
On 10/31/2011
On 1/11/2011 3:00 AM, James Starlight wrote:
I've done all of that
i have "posre_lipid.itp" - for 1 lipid ( posres for each of 50 atoms )
I've included this in the topology of the bilayer
; Include chain topologies
#include "gromos53a6_lipid.ff/forcefield.itp"
#include "dppc.itp"
; Include wa
James Starlight wrote:
I've done all of that
i have "posre_lipid.itp" - for 1 lipid ( posres for each of 50 atoms )
I've included this in the topology of the bilayer
; Include chain topologies
#include "gromos53a6_lipid.ff/forcefield.itp"
#include "dppc.itp"
; Include water topology
#includ
>
> Try minimizing again now with all bonds constrained using the output of
> the EM that ran. Generally, if EM crashes, your system contains some
> unresolvable clash or inappropriate geometry. Perhaps you have now relaxed
> the bad interactions sufficiently to proceed.
>
I had examined struct
Hi Laura,
I do not think Justin Lemkul's tutorial is suggesting extracting PMF using
SMD simulation. What is does that it uses SMD to generate the initial
configurations for different windows and then perform umbrella sampling
separately on each windows to subsequently extract the PMF using WH
Yes, I believe that is correct. I know that this is one way to get the
PMF using Gromacs. I am not sure if there is a way to use the Jarzinsky
equation explicitly to extract the PMF from just a sMD run with Gromacs.
On 10/31/2011 01:29 PM, Sanku M wrote:
using SMD simulation. What is does that
Laura Kingsley wrote:
Yes, I believe that is correct. I know that this is one way to get the
PMF using Gromacs. I am not sure if there is a way to use the Jarzinsky
equation explicitly to extract the PMF from just a sMD run with Gromacs.
One approach:
http://lists.gromacs.org/pipermail/gm
Thanks Mark!
It was actually what I did.
mdrun -rerun with well-chosen energy group exclusions only gives the
energy
between certain pairs of group, not the forces.
g_traj gives the overall forces not the force between certain pair.
Thanks a lot for any further idea to obtain the force for cert
I m using gromacs 4.5.3 version and trying to simulate a protein in liquid
media but I found problem in eqilibration step especially when I give
following command:
mdrun -deffnm nvt
.After giving this command it is showing error,i.e.,
There is no domain decomposition for 4 nodes that is compatibl
Anushree Tripathi wrote:
I m using gromacs 4.5.3 version and trying to simulate a protein in
liquid media but I found problem in eqilibration step especially when I
give following command:
mdrun -deffnm nvt
.After giving this command it is showing error,i.e.,
There is no domain decompositio
Hi James,
I usually use Swiss-PdbViewer (http://spdbv.vital-it.ch/disclaim.html). Despite
being an old and not well supported for any system, it is still a free and easy
to use and allows the building and mutating of residues in addition to
automatically adding missing atoms.
You can just bu
Greeting
I wonder if my MD simulation of a monomeric enzyme in WT and 3 mutated
forms has converged to equilibrium and simulation is suitable for analysis.
The 4 MD simulations are done in cubic water volume, 500 ps of steepest
descent minimization , with 100 ps of NVT ensemble and 100 ps of NPT
en
larif sofiene wrote:
Greeting
I wonder if my MD simulation of a monomeric enzyme in WT and 3 mutated
forms has converged to equilibrium and simulation is suitable for analysis.
The 4 MD simulations are done in cubic water volume, 500 ps of steepest
descent minimization , with 100 ps of NVT en
On 1/11/2011 5:40 AM, Tom wrote:
Thanks Mark!
It was actually what I did.
mdrun -rerun with well-chosen energy group exclusions only gives the
energy
between certain pairs of group, not the forces.
Did you use nstfout to actually write the forces?
g_traj gives the overall forces not the
On 1/11/2011 3:43 AM, Yuri Garmay wrote:
Try minimizing again now with all bonds constrained using the
output of the EM that ran. Generally, if EM crashes, your system
contains some unresolvable clash or inappropriate geometry.
Perhaps you have now relaxed the bad interactions
Dear Gromacs users,
I have built a protein embedded in popc bilayer and executed pdb2gmx using
charmm27 ff on the system and the toplogy file was created without errors,
but when wanted to minimise the system with grompp i am getting an error as
: unknown cmap torsion between atoms 8377 8379 8381
On 1/11/2011 1:24 PM, ram bio wrote:
Dear Gromacs users,
I have built a protein embedded in popc bilayer and executed pdb2gmx
using charmm27 ff on the system and the toplogy file was created
without errors, but when wanted to minimise the system with grompp i
am getting an error as : unknown
Hi Mark,
Thanks for the response.
I have built this system (protein in popc bilayer using charmm GUI) and
submitted the total built system to pdb2gmx, is this the reason for having
unknown CMAP torsion while executing grompp, by the way pdb2gmx doesnot
show any error. Cant the charmm gui built sys
On 1/11/2011 2:16 PM, ram bio wrote:
Hi Mark,
Thanks for the response.
I have built this system (protein in popc bilayer using charmm GUI)
and submitted the total built system to pdb2gmx, is this the reason
for having unknown CMAP torsion while executing grompp, by the way
pdb2gmx doesnot sho
Dear all,
I am low on disk space and need to delete trr files. I turned on -x option
in all runs so generated xtc files as well. Just wondering if xtc files
contain less information than trr ones which make xtc have less size. Am I
going to lose any information other than velocities?
Thanks,
J.
-
On 1/11/2011 3:30 PM, Juliette N. wrote:
Dear all,
I am low on disk space and need to delete trr files. I turned on -x
option in all runs so generated xtc files as well. Just wondering if
xtc files contain less information than trr ones which make xtc have
less size. Am I going to lose any in
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