Hello. ¿Have you removed periodicity?. Because you may only be seeing
traversal of water molecules among copies of the periodic system.
Lucio Montero
Ph. D. student
Instituto de Biotecnologia, UNAM
Mexico
El 08/08/13 07:39, Ondrej Kroutil escribió:
Dear GMX users.
I have done simulation
¿Did you change also the name of the “residue” (from 1MeOH to 1CH3OH (that is
the “residue” name appearing in the RTP file))?
Best regards
Lucio
From: Mina Madah
Sent: Tuesday, November 16, 2010 6:00 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] Atomtype CMET not found
Dear all
Independently of your ATP position, your system may explode or show
LINCS warnings if you use pressure and temperature coupling. I had these
problem, and corrected it removing the pressure coupling. Pressure
coupling will let your system expand in response to the heat, and if the
positions are
How can you calculate computationally charges for molecules containing
phosphates?
--
From: Ran Friedman, Biochemisches Inst. r.fried...@bioc.uzh.ch
Sent: Friday, March 27, 2009 2:35 PM
To: bije...@yahoo.com.br; Discussion list for GROMACS users
I don't know the conditions you use with your system, but sometimes there are
problems when you use pressure coupling in a system with positionally
restrained or fixed atoms.
Cheers.
Lucio.
From: Joe Joe
Sent: Friday, April 10, 2009 12:12 PM
To: Discussion list for GROMACS users
-atom. Jorgensen himself
uses OPLS-AA with TIP4P, so this is probably the best recommendation.
Most important, if you chose to use another combination, you basically
have to prove that this works as well (whatever that means...)
Mensaje citado por Justin A. Lemkul jalem...@vt.edu:
Lucio Montero
How about MOPAC to calculate the charges for 3-methyladenine (this molecule
has a charge +1) for using the G43a1 force field?.
--
From: Ran Friedman, Biochemisches Inst. r.fried...@bioc.uzh.ch
Sent: Friday, March 27, 2009 2:35 PM
To:
How can you test the ligands when you don't know if they REALLY bind to
the protein?
--
From: Ran Friedman, Biochemisches Inst. r.fried...@bioc.uzh.ch
Sent: Friday, March 27, 2009 2:35 PM
To: bije...@yahoo.com.br; Discussion list for GROMACS users
aa (protein
1: 376 aa, protein 2: 132 aa, protein 3: 20 aa, complex size 64x64x104
Angstroms) surrounded by 12 Ângstroms of water. I want to run the MD simulating
20 ns.
Best regards,
Lucio Montero
If you use periodic boundaries, the box size needs to be more than twice the
cutoffs, to avoid calculation errors. I found this advice in the manual. (I
though reading it was a time waste, but more time I was going to waste doing
a wrong 1 ns simulation on a big system).
Thanks very much.
Lucio Montero.
--
From: Justin A. Lemkul jalem...@vt.edu
Sent: Wednesday, February 25, 2009 5:55 AM
To: Discusson list for GROMACS users gmx-users@gromacs.org
Subject: Re: [gmx-users] OPLS-AA topologies for ATP/ADP.
Lucio
If your box is very big, VMD may run out all your computer's memory and
crash. You can copy your GRO file and erase some water molecules in the
middle of the GRO file copy, for you see the extremes of your water box.
Kind regards.
--
From: Mark
If you are doing simulated annealing, your system explode if you are heating
all the system (protein and water). Divide your system in protein and water
and heat only the protein.
--
From: Tsjerk Wassenaar [EMAIL PROTECTED]
Sent: Monday,
If you are using the GROMOS96, the forcefield files are ffG.*. ffgmx are
for the GROMACS forcefield (that is deprecated). The forcefield file titles
are listed in the file FF.dat in the gromacs topology directory. Here are
the contents of my FF.dat file:
11
ffG43a1 GROMOS96 43a1 force
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