You have to make sure of two things:
1- use a reference (gro or tpr) where the molecule is whole! The tpr is
prefered since the molecules are defined.
2- with such a reference and the option -mol you'll get a trajectory with the
protein as a whole.
On that trajectory you may apply more modi
I tried a couple of things according to your suggestions, but no luck so far
I used the following commands
1) trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -o trajout_mol.xtc
2) trjconv -f trajout_mol.xtc -s topol.tpr -pbc nojump trajout_nojump.xtc
no luck...If I use command 1) only the
On Feb 20, 2011, at 9:30 PM, Justin Kat wrote:
> Dear experts,
>
> I am still unable to overcome this error during the configuration:
>
> configure: error: cannot compute sizeof (off_t)
> See `config.log' for more details.
So what does config.log say about "cannot compute sizeof (off_t) ?"
Car
ok this does not make sense! Did you check your tpr file?
the command 1) should give you a trajectory where the molecules
are whole but jumping across the boundaries ... if it does not that
means that the tpr is fucky!
Try to visualize your tpr in vmd ... night give you some insight on
what is
Hi Evelyne,
> 1) trjconv -f trajout_dt2000.xtc -s topol.tpr -pbc mol -o trajout_mol.xtc
The option -pbc mol IIRC relates to the option for the unit cell
representation (-ur). To unbreak molecules using trjconv, you need to
have .tpr file and use the option -pbc whole.
> 2) trjconv -f trajout_m
Hi Bipin,
The file residuetypes.dat is quite different from aminoacids.dat. You
can paste the following into that file (first line is number of
entries, followed by so many residue names):
49
ABU
ACE
AIB
ALA
ARG
ARGN
ASN
ASN1
ASP
ASP1
ASPH
CYS
CYS1
CYS2
CYSH
DALA
GLN
GLU
GLUH
GLY
HIS
HIS1
HI
Thanks a lot Sir.
On Mon, Feb 21, 2011 at 15:26, Tsjerk Wassenaar wrote:
> Hi Bipin,
>
> The file residuetypes.dat is quite different from aminoacids.dat. You
> can paste the following into that file (first line is number of
> entries, followed by so many residue names):
>
> 49
> ABU
> ACE
> AIB
Dear Gromacs Users,
I would like to know if there is in gromacs an option how to calculate how
many contacts has a certain atom i(n a molecules of interest) with water
during the whole MD simulations (or at each step of MD).
Please could you advice me on this?
best,
Olga
--
gmx-users mailing lis
g_dist
On Feb 21, 2011, at 11:32 AM, Olga Ivchenko wrote:
Dear Gromacs Users,
I would like to know if there is in gromacs an option how to
calculate how many contacts has a certain atom i(n a molecules of
interest) with water during the whole MD simulations (or at each
step of MD).
Pleas
Or g_hbond -contact. Undfortuntely there are still issues with g_hbond
at the moment. Version 4.0.x seem to work better.
XAvier Periole skrev 2011-02-21 11.37:
g_dist
On Feb 21, 2011, at 11:32 AM, Olga Ivchenko wrote:
Dear Gromacs Users,
I would like to know if there is in gromacs an option
g_mindist -on (with suitable index groups) should also do the trick.
-Justin
Erik Marklund wrote:
Or g_hbond -contact. Undfortuntely there are still issues with g_hbond
at the moment. Version 4.0.x seem to work better.
XAvier Periole skrev 2011-02-21 11.37:
g_dist
On Feb 21, 2011, at 11:32
Thank you very much.
best,
Olga
2011/2/21 Justin A. Lemkul
>
> g_mindist -on (with suitable index groups) should also do the trick.
>
> -Justin
>
>
> Erik Marklund wrote:
>
>> Or g_hbond -contact. Undfortuntely there are still issues with g_hbond at
>> the moment. Version 4.0.x seem to work bett
Hello, gods of gromacs,
I have ported the parmbsc0 modifications to a new gromacs force field, based on
the amber99sb.ff, this involves adding a new carbon atom (CI) to be used in the
C5' of nucleotides.
Everything is working perfectly (to my astonishment) and I am confident of all
of the mo
So I used mindist for a certain group of molecules which is surrounded by
water. I got plot number of contacts versuc sumulation time. According to
what I see in a distance < 0.6nm at certain frame there are on average 150
contacts.
Actually how the programm calculates the number of contacts, if
Olga Ivchenko wrote:
So I used mindist for a certain group of molecules which is surrounded
by water. I got plot number of contacts versuc sumulation time.
According to what I see in a distance < 0.6nm at certain frame there
are on average 150 contacts.
Actually how the programm calculates
Skickat från min iPhone
18 feb 2011 kl. 21:10 skrev Matthew Zwier :
> Dear GROMACS developers and users,
>
> Our research group is interested in performing GBSA simulations with
> GROMACS, but we would need to perform them with a nonzero salt
> concentration. I was wondering if there are plan
Hello,
I read through the couple-intramol options (yes and no) good many times but
I can not still realize what is the difference and which option I should
select. I am having a hydrocarbon system (polyethylene in hexane as
solvent). Can anyone help me understand these options please? (in plain
en
Hello,
I am trying to calculate the diffusion coefficient of a molecule in water using
g_msd, and I have a doubt:
I get 3 different values when I use the trajectory directly from the
simulation, the trajectory using PBC conditions, and the "fitted trajectory".
Which would be the correct value fo
Dear all,
I would like to calculate the potential of mean force between two molecules
in aqueous solution using the pull code. For a start i performed a number
of calulations with a couple of very simple model systems with settings
loosely based on the example in the gmx tutorial section (see m
Hassan Shallal wrote:
Dear Gromacs users,
While I was using Gromos force field in simulating a protein in explicit
solvent, I used the following parameters:
*rcoulomb = 1, rlist =1, rvdw = 1.4*
*Electrostatitcs : PME*
*VDW : Twin range cutoff*
The above situation will not allow the calc
Dear Gromacs users,
While I was using Gromos force field in simulating a protein in explicit
solvent, I used the following parameters:
rcoulomb = 1, rlist =1, rvdw = 1.4
Electrostatitcs : PME
VDW : Twin range cutoff
The above situation will not allow the calculation of any long-range
electr
Jianguo Li wrote:
Dear all,
I want to get the PMF of my peptide across the membrane bilayer. First I
pulled my peptide across the membrane and then did windowed umbrella
sampling along the reaction coordinates which is the z-distance between
peptide and membrane. However, I found that sampl
Dear all,
I want to get the PMF of my peptide across the membrane bilayer. First I pulled
my peptide across the membrane and then did windowed umbrella sampling along
the
reaction coordinates which is the z-distance between peptide and membrane.
However, I found that sampling is not sufficient
Jianguo Li wrote:
Thanks Justin.
I tried your suggestions by either increase more windows and change the
force constant, but it seems the samplings are still bad in some
windows. When I did pulling in (0 0 1) direction and a reverse pulling
in (0 0 -1) direction, I got different configuratio
Hello all
I obtained a top file after running the "amb2gmx.pl" script,but I feel some
errors in this top file.
The functype of the [dihedral] is 3 in this top file,but the [pairs] part aslo
presence in it. And the
manual is point that "with the Ryckaert-Bellemans potential the 1-4
interactions
Thanks Justin.
I tried your suggestions by either increase more windows and change the force
constant, but it seems the samplings are still bad in some windows. When I did
pulling in (0 0 1) direction and a reverse pulling in (0 0 -1) direction, I got
different configurations at certain reaction
Looking at http://www.brunsteiner.net/tbut-pmf.gif you seem to be
getting exactly what I would expect. The difference is the entropy
term. Note that the spherical shell increases volume as r increases
for pulldim YYY but this effect is absent for pulldim NNY. This is why
you can correct as
Thanks for your comments, Justin.
Using timestep of 20 fs, in each window the simulation runs for 100 ns CG time.
The pulling rate is 0.001 nm/ps. Is it too fast?
My system is a little different. My peptide is highly positively charged. The
NMR experiments show that the conformation of the pept
Jianguo Li wrote:
Thanks for your comments, Justin.
Using timestep of 20 fs, in each window the simulation runs for 100 ns
CG time. The pulling rate is 0.001 nm/ps. Is it too fast?
Let me clarify things, since I'm not convinced I understand your procedure.
You generate a series of configu
Sounds like unconverged sampling. You would be astounded how long
systems like this can take to converge. An all-atom simulation like
this can easily require >10 us (microseconds!) per umbrella. I don't
know about martini, probably a lot less.
Chris.
-- original message --
Thanks Justin.
Dear All:
I am using OPLS force field (OPLS FF) to do molecular dynamics
simulations. My system contains DPPC lipid, protein and a small
molecule. I have the following questions:
1, where can I get the topology files for the DPPC lipids?
2, How to prepare the topology files for the small m
Dear Justin
My simulation system contains protein, dna and water.
I used your script already for obtaining %exist hydrogen bonds between
protein and dna:
#!/usr/bin/perl
#
# plot_hbmap.pl - plot the probability of finding a particular hydrogen bond
# based on several input files:
# 1. coordina
7 and 8 have nothing to do with OPLS-AA.
As the text tells you, it is the Encad forcefield
(http://www.sklogwiki.org/SklogWiki/index.php/ENCAD_%28force_field%29)
So that then leaves you with the OPLS-AA for you to use :-)
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash In
Hello,
I'm investigating the diffusion coefficient of gases in liquids. Therefore, I
insert some molecules with the genbox tool in an equilibrated system. After a
NPT run to adjust the density, I'm running an NVT simulation to calculate the
diffusion coefficient (g_msd). MSD of the liquids are
Thanks Justin and Chris and sorry for confusing interpretation.
Let me make it more clear. My peptide is flexible Martini beads, and highly
positively charged. My membrane is a mixture of negatively charged lipids (25%)
and zitterionic lipids(75%). So there is strong electrostatic attraction
be
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