Dear all
I am doing simulation of membrane protein ,for this first i
did the concatanation of protein in lipid bilayer in proper orientation
after that I am using inflategro script of teleman sir
but after doing first step successfully I am getting problem in second step
i,e ene
Dear all
I am doing simulation of membrane protein ,for this first i
did the concatanation of protein in lipid bilayer in proper orientation
after that I am using inflategro script of teleman sir
but after doing first step successfully I am getting problem in second step
i,e ene
Hi Bram,
Check the creation times for topol.tpr and minimized.gro. First test
the assumption that the former was created later than the latter. If
it's not, then check the grompp output for errors. Maybe pasting it
here can help.
Cheers,
Tsjerk
On Thu, Apr 16, 2009 at 10:57 AM, Hoof, B. van wr
nitu sharma wrote:
Dear all
I am doing simulation of membrane protein ,for this
first i did the concatanation of protein in lipid bilayer in proper
orientation after that I am using inflategro script of teleman sir
but after doing first step successfully I am getting probl
Hi Bram,
So to echo Justin, it's really better if you use distinct names for
the files generated at each step. The -deffnm option to mdrun can be
helpful there too. This will help you avoid mistakes like this _and_
will ensure you have all the files available in case you need to check
where things
Hi Justin,
Thanks for your answer. I am afraid, however, that the problem is then somewhat
different. Using
grompp -f martini_md1.mdp -c minimized.gro -p martini.top -maxwarn 10
should have created a new topol.tpr, should it not? It did so in previous times
at least.
If someone knows where I a
Yes, indeed. The file topol.tpr was not re-created when I used grompp. In fact,
an error was thrown by grompp stating file input/output error: minimized.gro
I am embarrased to say that I had used the command
> grompp -f martini_md1.mdp -c minimized.gro -p martini.top -o membr.tpr
> -maxwarn 10
i
Dear all,
When we do a MD simulation, we always set a cutoff
of non-bonded interactions, e.g. r=1.2 nm. When the
simulation finished, we can use the command
g_energy -f ener.edr -s ... to abtain the non-boned
energy of the system. My question is whether the non-bonded
energy values depe
Hi,
This problem has been discussed for decades in the literature. There are
approaches such as PME and reaction field to deal with the long-range
electrostatics.
Ran.
Dechang Li wrote:
> Dear all,
>
> When we do a MD simulation, we always set a cutoff
> of non-bonded interactions, e.g. r
Hello,
I have a question about the following grompp 4.0.4 warning:
"You are using an absolute reference for pulling, but the rest of the
system does not have an absolute reference. This will lead to
artifacts."
While I do realize that this is an excellent error message containing
lots of
Hi,
it was pointed out before that for Brownian Dynamics simulation, the
temperature calculated by g_energy does not match with the ref_t in
parameter file and it is almost double:
http://www.gromacs.org/pipermail/gmx-users/2007-June/028321.html ...
but unfortunately I find no follow-up to that po
>--
>
>Message: 3
>Date: Thu, 16 Apr 2009 14:11:51 +0200
>From: Ran Friedman
>Subject: Re: [gmx-users] the vdw and electrostatic energy
>To: Discussion list for GROMACS users
>Message-ID: <49e72087.8020...@bioc.uzh.ch>
>Content-Type: text/plain; charset=GB2312
>
>Hi
No. SR stands for short-range.
Ran.
>
> I did not mean that. I want to know that when we use g_energy in
> Gromacs to
> read the energy from the file ener.edr, does the cutoff affect the values
> of the energy? For example, when the cutoff is set to 1.2 nm and the PME
> method
> is
Apparently some versions of make do not handle my make files the same way that
the version of make I use does. The attached Makefile might help in such cases.
Sincerely,
--
Bruce D. Ray, Ph.D.
Associate Scientist, and Operations Director
NMR Center
IUPUI
Physics Dept.
402 N. Blackford St.
Ind
Hi Justin:
1) EXTREMELY IMPORTANT: I already know of 1 person, but is anyone alergic to
either Iodine or Chlorine?
No, I am not alergic to those compounds. The only thing that I am alergic is
Penicillin and Ampicilin.
2) Any other medical problems?
No
3) An Emergency contact person.
Fernand
Hello all,
I'm trying to help a student build gromacs_4.0.4 on a MacBook Pro
running 10.5. The program configures with out a hitch, but compiling
with the make command ends in a recursive error. It seems that it's
not finding something that it should have installed itself, but I
wouldn't
Ken Rotondi wrote:
Hello all,
I'm trying to help a student build gromacs_4.0.4 on a MacBook Pro
running 10.5. The program configures with out a hitch, but compiling
with the make command ends in a recursive error. It seems that it's not
finding something that it should have installed itself,
Ken Rotondi wrote:
Hello all,
I'm trying to help a student build gromacs_4.0.4 on a MacBook Pro
running 10.5. The program configures with out a hitch, but compiling
with the make command ends in a recursive error. It seems that it's not
finding something that it should have installed itself
Yes sir, that was the problem
Many thanks,
Ken
On Apr 16, 2009, at 3:33 PM, David van der Spoel wrote:
Ken Rotondi wrote:
Hello all,
I'm trying to help a student build gromacs_4.0.4 on a MacBook Pro
running 10.5. The program configures with out a hitch, but
compiling with the make comm
Dear All:
I wanted to get the viscosity of my simulated polymer system. From the
manual it said that : GROMACS also has a non-equilibrium method for
determining the viscosity" (page 123) Does this mean I just need to do
a separate non-equilibrium MD run? In terms of mdp file, I just need
to add th
Hi all users,
I have used the position_restraints to restrict some atoms' activity but always
it shows that Segmentation fault (core dumped).
I can not fix this problem after trying many methods and hence, I just wonder
whether there are some other ways to restrict the atoms' movement in the
g
He, Yang wrote:
Hi all users,
I have used the position_restraints to restrict some atoms' activity but always
it shows that Segmentation fault (core dumped).
It's 99% likely that this is not all that is going on - you have to read
the end of the .log file and the standard output/error to dia
Suman Chakrabarty wrote:
Hi,
it was pointed out before that for Brownian Dynamics simulation, the
temperature calculated by g_energy does not match with the ref_t in
parameter file and it is almost double:
http://www.gromacs.org/pipermail/gmx-users/2007-June/028321.html ...
but unfortunately I f
Tsjerk, your good reference helped me to understand the set_pbc and pbc_dx
functions from g_dist... I changed few lines of it and my problem was
solved. Thank you.
Cheers. Fernando.
2009/4/14 Tsjerk Wassenaar
> Hi Fernando,
>
> Just bear in mind that these lattice vectors are just translation
Dear gmx users,
While running final md run some unexpected message is coming which i am not
able to understand..
Pls help.
I am attaching md.log file with this mail.
--
Sheetal Arora
M.Tech(Biotechnology & Medical Engg)
NIT Rourkela
Log file opened on Fri Apr 17 09:37:41 2009
Host: localhost1.l
Sheetal Arora wrote:
Dear gmx users,
While running final md run some unexpected message is coming which i am
not able to understand..
Pls help.
I am attaching md.log file with this mail.
That's just normal output with no diagnostic message about the reason
for incomplete termination - if ind
Yanmei Song wrote:
Dear All:
I wanted to get the viscosity of my simulated polymer system. From the
manual it said that : GROMACS also has a non-equilibrium method for
determining the viscosity" (page 123) Does this mean I just need to do
a separate non-equilibrium MD run? In terms of mdp file,
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