Hi Tsjerk and Mark,
thanks for the answers.
The topologies differ in one atom which is changed from NR in the old
topology to N in new topology and also, there is one dihedral angle not
defined in the old topology and then zero is used by grompp. In the new
topology, the dihedral is defined
Hi,
I would also like to add that when simulating the protein alone, I
observe rising energies in md simulation. Only minor differences in
energy minimisation energy values are observed, if the protein is first
energy minimised in vacuum or not. The energy minimisation in a water
box goes
From: Chris Neale [EMAIL PROTECTED]
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
To: gmx-users@gromacs.org
Subject: [gmx-users] pbc_dx specific compilation or linking problem
Date: Thu, 22 Mar 2007 19:15:25 -0400
I have installed gromacs successfully on many systems.
Hie people,
Can somobody please tell me how the paramaters for
lipid-GROMOS interactions in lipid.itp file has been
scaled?
warm regards,
Pri...
Finding fabulous fares is fun.
Let Yahoo! FareChase search
Erik, Berk,
Hi David,
It doesn't matter - we just check if it is set at all, i.e. whether
getenv(NO_SHAKE_ERROR) returns NULL or not.
I still get PDB files written out due to shake errors using mdrun
-rerun in 3.3 when running after doing setenv NO_SHAKE_ERROR.
David
Cheers,
Erik
On
Hie! When I try to make energy minimization of protein-ligand system in water
box, after beginning the protein immediately moves out of water box leaving a
hollow in water and ligand in the hollow, after that minimization continues.
How could it be explained?
Best regards!
Alexandr,
This really is a bit too much. It's just as if you guys are trying to
push us over the edge. It gets so hard to stay polite at this point...
Read the archives on the gromacs user list. Search for protein out
of box or something, and you'll get plenty of hits, even some from
just a few
Hi,
We'll see how the new list footer appears - I just added a link with
to the archive search page :-)
Cheers,
Erik
On Mar 23, 2007, at 1:03 PM, Tsjerk Wassenaar wrote:
Read the archives on the gromacs user list. Search for protein out
of box or something, and you'll get plenty of
Hi,
Ah, then it's probably because of the rerun. I bet we're never making
a call to low_constrain with bInit set, which means the variable
isn't set.
Try this:
Edit low_constrain() in constr.c so to make bDumpOnError an integer
instead of boolean, and initialize it to -1.
Then cell
Hi Chris:
I´ve created my own dppc.itp using the ffG53a5 force field. I did that
running only a dppc lipid of the membrane that is available on
Tieleman's site and i included it on my topology file and of course
put in it the number of dppc molecules . i haven´t had any problem
with this
dear all,
in the force field file for residue types ffG53a6.rtp, one of the two
potentials for the so-called beta dihedral angle for the nucleic acid
backbone atoms P-O5'-C5'-C4' is missing.
this dihedral potential term is indicated in the article published with
the GROMOS force field 45A4
Erik,
Thanks. That does it. I assume you guys will put something like this into CVS?
Thanks again -- this is a lifesaver. I've had a couple hundred of
these trajectories to reprocess and haven't been able to do it without
filling my disk with unwanted pdb files.
David
On 3/23/07, Erik Lindahl
Carlo,
I have read in CSC Course Material that it is possible
to do not add counter ions in a charged system with
PME electrostatics , because gromacs (3.3.1 ?) adds a
background uniform charge to neutralize the system.
Is this neutralization correct and used in literature?
I can't say much
Hi,
On Mar 23, 2007, at 5:10 PM, David Mobley wrote:
Erik,
Thanks. That does it. I assume you guys will put something like
this into CVS?
Certainly - but I figured it would be way faster for you to check
that it solved the issue rather than me putting it on my to-do list :-)
Hi,
Gromacs correctly accounts for both charge and dipole corrections,
but as David says that is just the mathematical part of the problem.
A decade ago it was a pain to equilibrate ions in the system, but
today it's fairly straightforward with an equilibration of 5-10ns. I
can only
Synopsis:
1. some versions of gcc are problematic for pbc_dx
2. apt-get edgy/universe gromacs 3.3.1-1 may have a broken pbc_dx
3. Detail that you requested (probably can be ignored)
###
1. Based on your reply I have downgraded my version of gcc and this has
solved the problem.
The compiler
dear all,
there are errors in the code regarding 1) the equation for kappa, which
is used for the reaction field method; and 2) in the calculation of the
ionic strength.
1) in rf_util.c kappa is calculated as
*kappa = sqrt(2*I/(EPSILON0*eps_rf*BOLTZ*Temp));
but the factor 2 in the square
Daniela S. Mueller wrote:
dear all,
there are errors in the code regarding 1) the equation for kappa, which
is used for the reaction field method; and 2) in the calculation of the
ionic strength.
1) in rf_util.c kappa is calculated as
*kappa = sqrt(2*I/(EPSILON0*eps_rf*BOLTZ*Temp));
but
Hello,
I just installed Gromacs on my windows machine under cygwin, and
everything seemed to go fine with the installation and whatnot. Initially,
when I tried to run a simulation, I obtained the error that Gromacs found the
number of coordinates in my .top file to be 0, because it could not
Tsjerk Wassenaar wrote:
Alexandr,
This really is a bit too much. It's just as if you guys are trying to
push us over the edge. It gets so hard to stay polite at this point...
Steady on... it's not each individual new user's fault that they're part
of a pattern of behaviour that can be
Erik Lindahl wrote:
Hi,
We'll see how the new list footer appears - I just added a link with to
the archive search page :-)
Most new users won't see this until *after* they post their first
request - if ever. How about including it on whatever Welcome email
gets sent as well?
Mark
Hi,every one. I intended to do some coarse grain simulation work ,however my
systen always echo :
Fatal error: number of coordinates in coordinate file (conf.gro, 12032) does
not match topology (topol.top, 0)
I put the inputfiles in my attachment ,can anyonehelp me?
Hi,every one. I intended to do some coarse grain simulation work ,however my
systen always echo :
Fatal error: number of coordinates in coordinate file (conf.gro, 12032) does
not match topology (topol.top, 0)
I put the inputfiles in my attachment ,can anyonehelp me?
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秦姗姗 wrote:
Hi,every one. I intended to do some coarse grain simulation work ,however my
systen always echo :
Fatal error: number of coordinates in coordinate file (conf.gro, 12032) does
not match topology (topol.top, 0)
There's a problem with the formatting of your .top file. Go back and
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