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Chris,
I too rely heavily on the Berendsen methods for T- and P-coupling, and have
always found them satisfactory. I have not seen much beyond the casual
references to the fact that N-H T-coupling and Parrinello-Rahman P-coupling are
superior in terms of membrane simulations. I have tried bo
Hi Justin,
I wonder if you could expand upon the following statement, or perhaps
offer some links or references.
"Some argument can be made that N-H is more applicable to membrane
simulations."
I am interested because I use a Berendsen thermostat for membrane
simulations. To be entirely
I have used the Berendsen method almost exclusively in my simulations, and it is
widely used in most of the literature I read. While the argument can be made
that Nose-Hoover gives a result closer to the true ensemble than Berendsen, I
think both are sufficient for simple protein in water simul
David van der Spoel wrote:
I work with a protein where 3 CYS redisidues make bond with a Zn atom by
its SG atoms and HIS redisidue makes bond with a Zn atom by its NE2 in
active site
I want to use deprotonated “cys”. In manual for “pdb2gmx “ clearly says
on option of choosing Cys proto
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Hi Lin!
I personally feel increasing the temperature in increments better than
giving sudden temperature jump to protein. Regarding temp coupling, both
have their limitations. Berendsen is a weak coupling, so can be used for
initial runs. Later you can use Nose-Hoover after the proper
equilib
Please search in the mailing list archive.
It's a problem of the g_wham and there was a fixed version from David
Bostick of Scripps.
Chenyue
On Mon, Jul 21, 2008 at 12:04 PM, crascgap <[EMAIL PROTECTED]> wrote:
> Hi everyone.
>
> I have exactly the same problem as user VENKATESH HARIHARAN from
>
Hi everyone.
I have exactly the same problem as user VENKATESH HARIHARAN from
our gmx-user list.
I am running this command to calculate the pmf:
mdrun -s system.tpr -pi umbrella.ppa -po umbrella.1.0.0.ppa -pn index.ndx -pd
umbrella.1.0.0.pdo -deffnm umbrella.1.0.0 -v &
And then I get this .pdo
I work with a protein where 3 CYS redisidues make bond with a Zn atom by
its SG atoms and HIS redisidue makes bond with a Zn atom by its NE2 in
active site
I want to use deprotonated “cys”. In manual for “pdb2gmx “ clearly says
on option of choosing Cys protonated state possibility but wh
Hi
My system has been dealt with minimisation and the system was kept
constant at 0 K.
Then, I want to increate the temperature to 300 K using the Berendsen
thermostat.
Should I increase the temperature of the system step by step... ?
increase temp from 0 K to 50 K
5
Hello all,
I am trying to make an addition to mu ffG43a1.rtp file for the molecule GDP.
I have read the entry:
http://www.gromacs.org/pipermail/gmx-users/2007-December/031139.html
which gives the topology for GTP. I would like to know how the parameters for
the GTP topology were found so that
Hi,
You did not specify for which type of vdw and electrostatics you want this
option.
For plain cut-off's it does not make sense.
In version 3.3 you can do what you want with the shift and switch options.
In the CVS version there are also Reaction-Field-zero and PME-Switch.
Berk.
> From: [EM
Hi All,
I want to simulate a system for which rvdw > rcoulomb and to account
for LJ interactions correctly rlist should be greater than rvdw (if
nstist != 1). For current gromacs setup rlist should be equal to
rcoulomb. I searched the mailing list and there has been several
discussions re
> I am a new user of gromacs. Recently, I have installed the gromacs-3.3.3
> software package on my computer. After installation was complete, I run the
> example of water in
> the online reference manual. The trajectory file is OK for the first time.
> But when I run it for the second time, and
Michael Hirtz wrote:
Hi Diego, hello other gmx-users participants,
Hi Michael, look for the bionano tutorial at VMD site. It will
instruct you how to use TCL to build your SiO surface from an "unit
cell".
In a near future they will release the "inorganic builder plugin" that
will make things
sarbani chattopadhyay wrote:
hi,
I have followed the process as told by Yuguan Mu.But while using the
comman "pdb2gmax"
I get the following error
Source code file: ter_db.c, line: 85
Fatal error:
Reading Termini Database: expected 3 items of atom data in stead of 1 on
line
N
> I am a new user of gromacs. Recently, I have installed the gromacs-3.3.3
> software package on my computer. After installation was complete, I run the
> example of water in
> the online reference manual. The trajectory file is OK for the first time.
> But when I run it for the second time, and
Hi All,
I want to simulate a system for which rvdw > rcoulomb and to account
for LJ interactions correctly rlist should be greater than rvdw (if
nstist != 1). For current gromacs setup rlist should be equal to
rcoulomb. I searched the mailing list and there has been several
discussions re
Hi Diego, hello other gmx-users participants,
> Hi Michael, look for the bionano tutorial at VMD site. It will
> instruct you how to use TCL to build your SiO surface from an "unit
> cell".
> In a near future they will release the "inorganic builder plugin" that
> will make things a LOT easier.
T
hi,
I have followed the process as told by Yuguan Mu.But while using the comman
"pdb2gmax"
I get the following error
Source code file: ter_db.c, line: 85
Fatal error:
Reading Termini Database: expected 3 items of atom data in stead of 1 on line
N NH314.0027-0.3000
I
Hello,I would like to know the switching potential function.In the manual the
potential function is Phi(r). Yet, this function has 1/nm**6 or 1/nm**12 units.
So this potential should be multiplied by a factor. I supposed that this factor
should be 6*4*epsilon*sigma**6 for the attractive part and
Please make sure to keep all correspondence on the gmx-users listserv so it can
be archived for others to use in the future. I may not ever arrive at a
solution, but others who read the thread may figure out what's going wrong!
ANINDITA GAYEN wrote:
dear sir,
I have tried to insert on
Thanks Berk,
yes, it was an older version. And I did have separate pme nodes when
posre was working. So now I'm trying out the new CVS version.
Andrea
On Jul 21, 2008, at 1:53 PM, Berk Hess wrote:
Hi,
There was a bug with PME and position restraints in the CVS version,
but that has been
Hi,
There was a bug with PME and position restraints in the CVS version,
but that has been fixed a month ago. This bug has exactly the behavior
you describe, posres should work ok with separate pme nodes (nnodes >= 12),
but not without (1 < nnodes < 12).
So I assume you are not using the most rec
Hi,
The oscillations are normal.
Berk.
Date: Thu, 17 Jul 2008 11:59:12 -0400
To: gmx-users@gromacs.org
From: [EMAIL PROTECTED]
Subject: [gmx-users] Constraint Pulling - Oscillating Forces
Hello,
I am running constraint pulling on a
peptide chain. After the run, the pull.pdo file outputs t
Hello,the pairs potential is a (classic) lennard jones potential till the value
of table extension. The problem in my example was in the precision of the value
of sigma. Under the pairs section I was able to put the value 0.23160, yet I
could not in the gro file for the coordinates of the atoms,
Hi Gerrit,
I am having the same problem in 32-bit machine. The error message is :
cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -malign-double
-funroll-all-loops -o mdrun glaasje.o gctio.o init_sh.o ionize.o do_gct.o
relax_sh.o repl_ex.o xutils.o compute_io.o md.o mdrun.o ge
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