Are you running constant pressure? If so, not surprising the box is shrinking,
since it is a vacuum. You should use constant volume.
Also, you cannot change the values of those settings you have within the .mdp
unless you have a good reason to and/or it is allowable by the forcefield.
These
On Mon, May 7, 2012 at 10:17 AM, Bala S wrote:
> Justin and Anirban,
>
> I have another query on membrane simulation following your tutorials.
>
> How do I insert only a part of protein into the lipid bilayer and carryout
> the simulation?
>
editconf with -box option helps you to orient your pro
Dear Gromacs users,
I am using GROMACS 3.3.2. I have a problem in setting the cut off of my MD-run.
I want to see the interaction between some small atoms keeping them inside a
periodic box without adding any solvent; i.e interaction between the atoms in
the vacuum.
I have a total of 18-25 atoms
Justin and Anirban,
I have another query on membrane simulation following your tutorials.
How do I insert only a part of protein into the lipid bilayer and carryout
the simulation?
Thanks
Bala S
--
View this message in context:
http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-U
RDF = probability function
Methylene density (number in the box (Nt) divided by the box volume),
multiplied by probability (RDF) and shell volume (r+dr) calculates number of
methylenes (Nm) within a given shell.
Fraction = Nm/Nt
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Dear Dr. Warren,
Thank you very much from your help, but I want to calculate the fraction of
methylenes in this distance to COM. How do I obtain this fraction in this
distance by RDF, Please?
Thank you again.
Best Regards
Dina
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gro
All right.
Thank you so much.
Shima
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Sunday, May 6, 2012 11:32 PM
Subject: Re: [gmx-users] Topology parameters
On 5/6/12 2:36 PM, Shima Arasteh wrote:
> IS the parameters for a residue in
Dear Justin,
The Jorgensen group have already published results for
aniline and DMA using the OPLS-AA parameters. I am using the charges from
their publication ( R. Rizzo and W.L.Jorgensen, J.Am.Chem.Soc., 1994, 121,
4827-4836). Even after several crosschecks I have not been able
On 7/05/2012 5:50 AM, Marcelo Lopez wrote:
For sure, this wouldn't happened if the information to run all the
Gromacs features were clearly explained in the place where should be:
the manual.
Life would be good if everything was perfect, but when you're relying on
free software provided by lar
Via the methylene - COM RDF.
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is
On 5/6/12 3:45 PM, Lara Bunte wrote:
Hi
You said:
The blank lines will be filled in with existing parameters from [angletypes] in
ffbonded.itp.
I let the lines empty and I got an error at the first grompp, before energy
minimization. grompp missed this empty lines. Here a part out of the
For sure, this wouldn't happened if the information to run all the
Gromacs features were clearly explained in the place where should be:
the manual.
Next time save some words and use your time to do a better
documentation job... unless you're trying to have some advantage...
Cheers!
2012/5/5 Mark
Hi
You said:
>The blank lines will be filled in with existing parameters from [angletypes]
>in ffbonded.itp.
I let the lines empty and I got an error at the first grompp, before energy
minimization. grompp missed this empty lines. Here a part out of the errors:
ERROR 28 [file topol.top, line 2
On 5/6/12 2:36 PM, Shima Arasteh wrote:
IS the parameters for a residue in CHARMM36 and CHARMM27 the same?
I would suggest you do a bit of reading about the CHARMM force field hierarchy
and why they are named as they are. If you're parameterizing a new residue you
can do it for either, or
On 5/6/12 11:42 AM, Debayan Chakraborty wrote:
Dear Colleagues,
I am trying to build a well equilibrated solvent box
of aniline and N,N dimethyl aniline using the OPLS-AA parameters. I have built
my topolgy files by closely following that given for 2-chloroaniline in
IS the parameters for a residue in CHARMM36 and CHARMM27 the same?
Thanks in advance,
Shima
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Saturday, May 5, 2012 9:16 PM
Subject: Re: [gmx-users] Topology parameters
On 5/5/12 11:39 AM,
Dear Colleagues,
I am trying to build a well equilibrated solvent
box of aniline and N,N dimethyl aniline using the OPLS-AA parameters. I
have built my topolgy files by closely following that given for
2-chloroaniline in the molecule and liquids database of virualchemistry
On 6/05/2012 9:08 PM, amit banerjee wrote:
Dear Gromacs Users,
I am trying to install gromacs 4.5.5
version in a CENTOS 5.4 machine with FFTW 3.3.1.
To do so, I have downloaded both the tar.gz files in root and tried to
install them as per the standard installatio
Dear Gromacs Users,
I am trying to install gromacs 4.5.5 version in
a CENTOS 5.4 machine with FFTW 3.3.1.
To do so, I have downloaded both the tar.gz files in root and tried to install
them as per the standard installation protocol.
Unfortunately i am receiving the
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