Dear Justin, gmx users,
I forgot to write, but I added these new residues to aminoacids.rtp.
Maybe I need to add them also to aminoacids.r2b? How to do it correctly?
Just new lines in it or add them to lines of Gly and Lys? So, I suppose it
is all steps in
Dear Gromacs-users,
I would like to add a new bond type to the ffbonded.itp of the Gromos53a6 force
field. For that, I tried to obtain the force constant for my new bond by
performing vibrational frequency calculations with Gaussian. With that, I
obtained the force constant in mDyne/A.
My
Hi Felix
Take a look to 4.2.1 section in the manual. Gromos force constants (k^b)
has this extra nm-2 factor because they are defined as:
2 k^b bij^2 = k^{b,harm} (equation 4.39 in the manual version 4.5.4)
So you have to divide your derived harmonic force constants (in
KJ/(mol*nm^2) by 2
Hey Javier,
Thank you very much!
I already read the manual, but somehow didn't get the point. Now its clear,
thanks.
Felix
Von: gmx-users-boun...@gromacs.org im Auftrag von Javier Cerezo
Gesendet: Mi 06.07.2011 09:40
An: gmx-users@gromacs.org
Betreff: Re:
Hi!
Yes, I did! Had to look up a conversation between me and the Tinker developers
about precisely this.
The values are indeed not the original ones, but rather developed internally by
Tinker people so to minimise differences between analytical surface areas and
GB, given the HCT-algorithm
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Yulian Gavrilov wrote:
Dear Justin, gmx users,
I forgot to write, but I added these new residues to aminoacids.rtp.
Maybe I need to add them also to aminoacids.r2b? How to do it correctly?
An .r2b entry is unnecessary in this case; these files are only used to
standardize force
Per Larsson wrote:
Hi!
Yes, I did! Had to look up a conversation between me and the Tinker
developers about precisely this.
The values are indeed not the original ones, but rather developed internally
by Tinker people so to minimise differences between analytical surface areas
and GB, given
Hi all,
As per Justin's suggestion , I have created a rtp entry for primed THY
residue..which is like this ..
[ DT5P ]
[ atoms ]
H5THO0.44220 1
O5'O-0.63180 2
C5'CT -0.00690 3
H5'1H10.07540 4
H5'2
Singh wrote:
Hi all,
As per Justin's suggestion , I have created a rtp entry for primed THY
residue..which is like this ..
[ DT5P ]
[ atoms ]
H5THO0.44220 1
O5'O-0.63180 2
C5'CT -0.00690 3
H5'1H10.07540
Amjad Farooq wrote:
Hello Justin,
Thank you for your insights into the g_dist command. I am becoming quite
an expert on it now!
I have another question for you and other GROMACS users:
I am doing MD simulation on a protein(35aa)-peptide(12aa) complex and I
noticed spikes in backbone RMSD
Hi Justin,
Thanks for quick response :)
Basically I don't want terminal H atom.. instead of that I want O+ at 3' end
and -CH2-O-PO3 at second. but it is appearing on both the ends... :(
Any suggestions?
Raghav
Research Scholar
IEMN, University of Science and Technology
Villeneuve d'ascq,
Please do not reply to the entire digest; the archive is horribly confusing as
it is. Let's not make it worse. Cut and paste any relevant text for your reply
and delete the extraneous stuff.
Singh wrote:
Hi Justin,
Thanks for quick response :)
Basically I don't want terminal H atom..
Hi All;
I did run simulation for 6 proteins for 200ns and the protein is just 18
residue each (have 6 of them) so 108 residues. i did run the simulation in
constant pressure then with Temperature 650K (for 20 ns) to make sure that are
separate and then run the simulation of the proteins
errabah fatima ezzahra wrote:
Hi All;
I did run simulation for 6 proteins for 200ns and the protein is just
18 residue each (have 6 of them) so 108 residues. i did run the
simulation in constant pressure then with Temperature 650K (for 20 ns)
to make sure that are separate and then run
Message: 1
Date: Tue, 05 Jul 2011 19:14:04 -0400
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] free energy calculations
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4e139abc.1030...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1;
Ragothaman Yennamalli wrote:
Message: 1
Date: Tue, 05 Jul 2011 19:14:04 -0400
From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu
Subject: Re: [gmx-users] free energy calculations
To: Discussion list for GROMACS users gmx-users@gromacs.org
Hi,
I do not understand the question. Specify what force field you used, what
parameters, what is Cl fix etc. etc and please send it back to the gmx-users
mailing list: gmx-users@gromacs.org
Regards,
Pär
6 jul 2011 kl. 15.59 skrev s_akbarshahi:
Hello Mr bjelkmar
I wanted to ask which
Dear Justin
I have prepared the pdb structure of an organic compound.
This compound is applied as a lable which covalently and specifically
attaches to a Cys residue of our protein.
I want to attache the label to the protein and simulate this complex.
what I need to know is that Can I manualy
Dear All
Problem : Distribution of sodium and chloride ions than chlorine fixed placein
center of box simulation
I wanted to ask which graphs the density of sodium is correct ?
Box : 2.65 *2.65 *2.65 nm
force field : AMBER99SB-ILDN
Number of Na : 10
Number of Cl : 9
Number of Cl fix : 1
Time
shiva birgani wrote:
Dear Justin
I have prepared the pdb structure of an organic compound.
This compound is applied as a lable which covalently and specifically
attaches to a Cys residue of our protein.
I want to attache the label to the protein and simulate this complex.
what I need to know
Hi Mark and everyone!
This has been a previous topic though and thanks Mark for the reply.
What I need to do is to calculate the potential energy (energy minimzation) of
a molecule at every fixed pairs of dihedrals (phi, psi). I did the suggestions
on
Mr Bernard Ramos wrote:
Hi Mark and everyone!
This has been a previous topic though and thanks Mark for the reply.
What I need to do is to calculate the potential energy (energy
minimzation) of a molecule at every fixed pairs of dihedrals (phi, psi).
I did the suggestions on
Thanks, Justin. I'll do experiments on that.
Thu, 7/7/11, Justin A. Lemkul jalem...@vt.edu wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] placing dihedral constraints
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Thursday, July 7, 2011, 1:32 AM
On 7/07/2011 2:53 AM, Saeid Akbarshahi wrote:
Dear All
Problem : Distribution of sodium and chloride ions thanchlorine fixed
placein center of box simulation
I wanted to ask which graphs the density of sodium is correct ?
Box : 2.65 *2.65 *2.65 nm
force field : AMBER99SB-ILDN
Number of Na : 10
On 7/07/2011 3:29 AM, Mr Bernard Ramos wrote:
Hi Mark and everyone!
This has been a previous topic though and thanks Mark for the reply.
What I need to do is to calculate the potential energy (energy
minimzation) of a molecule at every fixed pairs of dihedrals (phi, psi).
So you really
Dear All
Question :
Problem : Distribution of sodium and chloride ions than chlorine fixed placein
center of box simulation
I wanted to ask which graphs the density of sodium is correct ?
Box : 2.65 *2.65 *2.65 nm
force field : AMBER99SB-ILDN
Number of Na : 10
Number of Cl : 9
Number of Cl
- Forwarded Message -
From: Saeid Akbarshahi saeidakbarsh...@yahoo.com
To: gmx-users@gromacs.org gmx-users@gromacs.org
Sent: Wednesday, July 6, 2011 10:44 PM
Subject: Ion distribution around Cl fix
Dear All
Question :
Problem : Distribution of sodium and chloride ions than chlorine
Repeatedly posting the same message (especially after having been told that the
question is unintelligible) is both ineffective for you in terms of receiving an
answer and uninspiring for those who might try to help you.
Your question is poorly formed. Please re-phrase your objectives,
Also for additional performance benefit you can use atlas math library
and compile gromacs and fftw with additional cflags like '-mfpmath=sse -
msse_version' This will enable sse math (by default gcc generates i386 and
sse).
PS Also you can use CFLAGS=-O2 -pipe -march=native -mfpmath=sse -
I am trying to compile mopac with gmx for qmmm calculation purpose and found
the link
http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMMis
really helpful.
However I can only download the on of the two required fortran files,
gmxmop.f,but not the other, dcart.f. And since
Dear All
I want to simulate a boxfilledwater that includes 10 sodium ion and 9 chloride
ion .
a chlorine fixed placein center of box simulation to see how it affects the
distribution ions .
Two graphs were obtained for the distribution of ions than to Cl fix (chlorine
fixin center of box)
hello! http://marcioneves.com/gidbinnr.php?eqluckyid=f5ceY
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