Hi,
Is there any place to read how gromacs treats polarizable models?
The only thing I found in the official manual is that shells are
denoted as S in the topology. What is especially interesting for me
now is a concrete implementation and the ways of use.
Thanks in advance.
Vitaly
--
Vitaly V.
Hi,
Thanks for the your reply. I quite know that there is need for expertise to be
able to derive parameters, that's why i want to know if anyone already have the
gromos parameters for the oxy- and carbomonoxy- heme.
The references i've seen so far for related works in my literature search
Hi,
There are HEME entry in the ffG43a1-files that come with gromacs. Wether
it's oxy- deoxy- or other heme I do not know. At some point I used them
for a myoglobin simulation, but I don't remember the details.
/Erik
olaniyi yusuff skrev:
Hi,
Thanks for the your reply. I quite know
olaniyi yusuff wrote:
Hi,
Thanks for the your reply. I quite know that there is need for expertise
to be able to derive parameters, that's why i want to know if anyone
already have the gromos parameters for the oxy- and carbomonoxy- heme.
The references i've seen so far for related works
Dear all,
I am trying to simulate a two component system, and I would like to ask you the
two following questions:
1) Is it possible to use a different scaling factor (for the LJ and the
electrostatics) for each component?
2) Is it possible to use energy and pressure correction only for the
Vitaly V. Chaban wrote:
Hi,
Is there any place to read how gromacs treats polarizable models?
The only thing I found in the official manual is that shells are
denoted as S in the topology. What is especially interesting for me
now is a concrete implementation and the ways of use.
Our old SW
Dear all,
I am dealing with a POPC+PEPTDE+WATER system. Basic residues of the
peptide make hydrogen bonds with lipid headgroup (as reflected from g_rdf
analysis) and the number of hydrogen bonds formed can be calculated from
g_hbond program. Now, i want to calculate the % of trajectory
Hi,
You can use g_hbond -num and write a small script to calculate the
percentage of h-bond existence per frame by calculating the number of
frames for which a h-bond exists.
Good luck,
Ran.
Moutusi Manna wrote:
Dear all,
I am dealing with a POPC+PEPTDE+WATER system. Basic residues
Hi,
The xpm-file matches the [ hbonds ] index group in the index file spat
out by g_hbond. X:th line in the map is the h-bond given by the 4:th
entry in the index group. Be careful when matching the rows though,
because in the xpm file the first line of data is the bottom row of the
matrix
On Wed, 28 Oct 2009, Mark Abraham wrote:
Peng Yi wrote:
I am trying to simulate alkane melt and found out that gromacs and lammps
gave different results, particularly the bonded interaction energy.
I wonder if anyone has such experience. Thanks,
Even two installations of the same
Hey,
are you running single or double precision gromacs?
Afaik, depending on the circumstances the energy drift in gromacs can be
rather bad for single precision.
Alex
Peng Yi schrieb:
On Wed, 28 Oct 2009, Mark Abraham wrote:
Peng Yi wrote:
I am trying to simulate alkane melt and found
aherz wrote:
Hey,
are you running single or double precision gromacs?
Afaik, depending on the circumstances the energy drift in gromacs can be
rather bad for single precision.
Please refer to the gromacs 4.0 paper for a discussion of the drift.
If you want to compare energies you need the
Hi Peng,
Note that you're not using any bond constraints in Gromacs and a
timestep of 2fs may be too long.
Also, tau_t=0.02 seems too short for me.
With 1fs timescale the agreement seem good enough, but you didn't
include estimated errors so it's hard to tell. Also, I assume you run
GMX in
Hi, Ran,
I didn't use bond restraints. I checked that the bond length had a
Gaussian-like distributes, and the length range looked normal.
I estimated the fastest timescale in the system, which is the bond
ossilation period, around 16fs. Would that require as integration
timestep much
On Thu, 29 Oct 2009, David van der Spoel wrote:
aherz wrote:
Hey,
are you running single or double precision gromacs?
Afaik, depending on the circumstances the energy drift in gromacs can be
rather bad for single precision.
Please refer to the gromacs 4.0 paper for a discussion of the
Hi Peng,
The time scale should be much shorter than the fastest vibration. A rule
of thumb from the reference below is a factor of ten, but it would
depend on the precision. Running with double precision is shorter but I
didn't make benchmarks (perhaps other users have).
Appropriate values of
Dear GROMACS Gurus,
Is it possible to determine the adsorption energy of a single molecule in
a simulation? My simulation has a large number of gas phase molecules
distributed throughout a box with some molecules adsorbed on a graphene
sheet. I would like to compare the adsorption energy of a
darre...@ece.ubc.ca wrote:
Dear GROMACS Gurus,
Is it possible to determine the adsorption energy of a single molecule in
a simulation? My simulation has a large number of gas phase molecules
distributed throughout a box with some molecules adsorbed on a graphene
sheet. I would like to compare
Hi,
I am trying to calculate the PMF of an ion with Gromacs 4. I have read in the
Gromacs list that the pull code had been completely rewritten in the new
version of Gromacs, but I cannot find much information about the new way to use
this.
Reading the manual (pag 280) I can see: “The options
Rebeca García Fandiño wrote:
Hi,
I am trying to calculate the PMF of an ion with Gromacs 4. I have read
in the Gromacs list that the pull code had been completely rewritten in
the new version of Gromacs, but I cannot find much information about the
new way to use this.
Reading the manual
Justin A. Lemkul wrote:
Are you reading the right version of the manual? I can find no mention
of these old flags in the manual for version 4.
Scratch that, I did find the quoted phrase. Perhaps the manual can be updated
to have this erroneous information removed?
-Justin
--
Hi all!
I just wonder if anyone run (know solution) into a problem trying to project a
trajectory on the eigenvector(s) (with g_anaeig -proj ) from covariace matrix.
All projections I have calculated are nan. However, the eigenvalues are OK and
the g_anaeig -comp -v2 -eig2 -over options
) Why not to use topology of charged ASP residue side chaas starting
point?
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ASP residue side
chaas starting point?
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sunny mishra wrote:
Yes I did the same and when I see my system.gro file it gives me the
dimensions of the protein box half of the lipid bilayer box so that
means it should now be set in the center of the lipid bilayer. But after
I don't understand what you mean.
that when I run the
Hi,
I'm using GROMACS 4.0.5 to do a MARTINI simulation of a CG protein in a CG
water box, looking at the diffusion constant of the protein among other
things. I'm using the Nose-Hoover thermostat and Parrinello-Rahman barostat
with tc-grps = System. In CHARMM, a protein-in-water simulation with
Dear All:
When I submitted the md run, It gives me the following error:
Program mdrun, VERSION 3.3.3
Source code file: gmxfio.c, line: 607
Fatal error:
wrong string length 0 for string buf (source tpxio.c, line 1150)
I run the similar system before using the same md.mdp file. and it was fine.
Yanmei Song wrote:
Dear All:
When I submitted the md run, It gives me the following error:
Program mdrun, VERSION 3.3.3
Source code file: gmxfio.c, line: 607
Fatal error:
wrong string length 0 for string buf (source tpxio.c, line 1150)
I run the similar system before using the same md.mdp
what version is the tpr file? The one corresponding to mdrun 3.3.3?
What do you mean?
I used gromacs-3.3.3 before and now. the same system and I did not have the
problem before.
On Thu, Oct 29, 2009 at 2:06 PM, David van der Spoel
sp...@xray.bmc.uu.sewrote:
Yanmei Song wrote:
Dear All:
Alright. I have done thisI have made another lipid_newbox.gro file and
wrote same box vectors as of lipid.gro file
For LIPID :
editconf -f lipid.gro -o lipid_newbox.gro -c -box 13.29820 13.29820 6.59160
For Protein :
editconf -f protein.gro -o protein_newbox.gro -c -box 13.29820 13.29820
sunny mishra wrote:
Alright. I have done thisI have made another lipid_newbox.gro file
and wrote same box vectors as of lipid.gro file
For LIPID :
editconf -f lipid.gro -o lipid_newbox.gro -c -box 13.29820 13.29820 6.59160
For Protein :
editconf -f protein.gro -o protein_newbox.gro -c
On Oct 29, 2009, at 9:26 PM, Michael Lerner wrote:
Hi,
I'm using GROMACS 4.0.5 to do a MARTINI simulation of a CG protein
in a CG water box, looking at the diffusion constant of the protein
among other things. I'm using the Nose-Hoover thermostat and
Parrinello-Rahman barostat with
Michael Lerner wrote:
Hi,
I'm using GROMACS 4.0.5 to do a MARTINI simulation of a CG protein in a
CG water box, looking at the diffusion constant of the protein among
other things. I'm using the Nose-Hoover thermostat and Parrinello-Rahman
barostat with tc-grps = System. In CHARMM, a
Well yes I guess I am getting the same thing what I expected but now I am
little confused here and I don't know how to explain you this but I will
try.
Initially I aligned my protein using TMDET results and centered that at
ORIGIN and then I centered the lipid at origin using geom_center script
sunny mishra wrote:
Well yes I guess I am getting the same thing what I expected but now I
am little confused here and I don't know how to explain you this but I
will try.
Initially I aligned my protein using TMDET results and centered that at
ORIGIN and then I centered the lipid at origin
Dear Users:
I used all-bonds for constraints. My MD is dead right after i submit the
task. The error message is :
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 2.084475 (between atoms 23417 and 23431) rms 0.054595
bonds that rotated more than 30 degrees:
Yanmei Song wrote:
Dear Users:
I used all-bonds for constraints. My MD is dead right after i submit the
task. The error message is :
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 2.084475 (between atoms 23417 and 23431) rms 0.054595
bonds that rotated
Ok. I guess that makes sense. If you say I can send you my system.gro file
(after catting the system as per our recent conversation) and my protein.gro
and lipid.gro files (In which the protein is inserted before our
conversation) and if you visualize that in VMD you will get more idea of
what I
sunny mishra wrote:
Ok. I guess that makes sense. If you say I can send you my system.gro
file (after catting the system as per our recent conversation) and my
protein.gro and lipid.gro files (In which the protein is inserted before
our conversation) and if you visualize that in VMD you will
On Thu, Oct 29, 2009 at 5:38 PM, Justin A. Lemkul jalem...@vt.edu wrote:
I see you are using constraints = none, but are there any constraints
defined in the topology? If so, as noted in g_traj -h:
Option -ot plots the temperature of each group, provided velocities are
present in the
On Thu, Oct 29, 2009 at 5:31 PM, XAvier Periole x.peri...@rug.nl wrote:
On Oct 29, 2009, at 9:26 PM, Michael Lerner wrote:
I calculated temperatures with
g_traj -f md2.trr -s md2.tpr -n index.ndx -ot -ng 5
I did not know you could get the temperature throught g_traj ... the -ot
option
Yanmei Song wrote:
what version is the tpr file? The one corresponding to mdrun 3.3.3?
What do you mean?
I used gromacs-3.3.3 before and now. the same system and I did not
have the problem before.
Is your disk full?
Is this reproducable?
On Thu, Oct 29, 2009 at 2:06 PM, David van der
Dear Gromacs users,
I am experimenting the next problem on an infiniband-cluster (8
intel-cores per node, GROMACS compiled with icc 11.1, all run through
mvapich2):
I have a molecule (protein 498aa, solvated or in vacuum I get the same
problem at any box shape), when I try to SD minimize it with
To get g_energy to give you the temperature (or any other property) of a
specific group you need to have defined appropriate energygrps in your mdp
file. This is independent of the choice of groups you use for the
temperature coupling.
If you want to calculate these temperatures of the groups
Dear users,
I just have 2 queries
1) Is it safe to use united atoms constraint for positional restraining and
md simulation of an enzyme docked to the substrate? if yes, what is the KEYWORD
to be typed in the mdp file and in what way is it simpler than the all-bonds
constraint?
2) How can a
Dear users,
How is it possible to fix the number of solvent molecules and the size of the
box used so that I can maintain exactly the same environment for different runs.
For eg, if I have 84000 water solvent molecules and the dimensions of 6.7 6.73
4.71 nm; how can I use the same system for a
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