Justin, Mark,
Ok
not I've included posre only to the lipid.itp wich consist of parameters
for just 1 lipid
#ifdef POSRES_LIPID
#include posre_lipid.itp
#endif
to the minim.mdp I've included
define= -DPOSRES_LIPID; position restrain the lipids
As the result I have not obtained any
On 02/11/11, James Starlight jmsstarli...@gmail.com wrote:
Justin, Mark,
Ok
not I've included posre only to the lipid.itp wich consist of parameters for
just 1 lipid
#ifdef POSRES_LIPID
#include posre_lipid.itp
#endif
to the minim.mdp I've included
define=
Hi GROMACS users,
I have generated .prmtop and .inpcrd files using xleap module
of AMBER for a single chain of a membrane protein molecule containing a
modified residue. After that I have converted those files into .gro,.top
,em.mdp and md.mdp files with the help of acpype.py. But
If I do not use for insert ions into the water from genion and Ions put in
the file pdb whether Gromacs no problem with it ?
Whether the behavior of ions such as ions that enter via genion ?
4.pdb :
ATOM 1 CL CL 145 23.580 24.000 -0.020 1.00 0.00
ATOM 2 CL
Justin,
Could you tell me more about adding caps by amber tools?
1) I've found in that software ACE as well as other groups but they are not
standart
e.g ACE is below instead of simple CH3 group
949 HH31 ACE29 2.000 1.000 -0.000 1.00 0.00
ATOM950 CH3 ACE29
Hi all
I have generated a gro file from a traj.trr file using trjconv. When I
use gmxdump on the same traj.trr file to output a generic format history
file it seems that there is a discrepancy in the coordinates of some
atoms in a particular frame. Essentially I output frame 5 using trjconv,
then
Saeid Akbarshahi wrote:
If I do not use for insert ions into the water from genion and Ions
put in the file pdb whether Gromacs no problem with it ?
genion is not required. If you provide reasonable ion positions in the system,
there is no problem.
-Justin
Whether the behavior of
madhumita das wrote:
Hi GROMACS users,
I have generated .prmtop and .inpcrd files using xleap
module of AMBER for a single chain of a membrane protein molecule
containing a modified residue. After that I have converted those files
into .gro,.top ,em.mdp and md.mdp files with
James Starlight wrote:
Justin,
Could you tell me more about adding caps by amber tools?
1) I've found in that software ACE as well as other groups but they are
not standart
e.g ACE is below instead of simple CH3 group
ACE is an acetyl group, not a methyl. Those coordinates look fine.
On 2/11/2011 10:23 PM, Gavin Melaugh wrote:
Hi all
I have generated a gro file from a traj.trr file using trjconv. When I
use gmxdump on the same traj.trr file to output a generic format history
file it seems that there is a discrepancy in the coordinates of some
atoms in a particular frame.
Hey Justin and Gmx Users,
In Justin's tutorial (Protein ligand complex) the mdp files (for NVT and
NPT) consists of tc_grps when you specify two groups: Protein_JZR and
Water_and_ions:
tc_grps = Protein_JZ4 Water_and_ions
In the mdp files it is specified:
tc-grps = Protein_JZ4
On 2/11/2011 11:27 PM, Steven Neumann wrote:
Hey Justin and Gmx Users,
In Justin's tutorial (Protein ligand complex) the mdp files (for NVT
and NPT) consists of tc_grps when you specify two groups: Protein_JZR
and Water_and_ions:
tc_grps = Protein_JZ4 Water_and_ions
In the mdp files it is
Steven Neumann wrote:
Hey Justin and Gmx Users,
In Justin's tutorial (Protein ligand complex) the mdp files (for NVT and
NPT) consists of tc_grps when you specify two groups: Protein_JZR and
Water_and_ions:
tc_grps = Protein_JZ4 Water_and_ions
In the mdp files it is specified:
*Dear All,
Could anybody suggest me some books or notes or some
materials which will help me to understand the way gromacs algorithms work
i.e. how neighbor group search works e.t.c. I kindly request you to suggest
me other than the gromacs manual.*
*With Regards,
Ravi Kumar
Ok, ok ok :) Thank you both!
Steven
On Wed, Nov 2, 2011 at 12:29 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
Hey Justin and Gmx Users,
In Justin's tutorial (Protein ligand complex) the mdp files (for NVT and
NPT) consists of tc_grps when you specify two groups:
Hi Mark
My Apologies. Here is more info.
gmxdump -f traj.trr history
From history I take the coordinates at 250 ps and convert to gro file
say test.gro
trjconv -f traj.trr -dump 250 -o frame5.gro
I then compare frame5.gro with test.gro
Please find attached an excerpts of both files (in one
Ravi Kumar Venkatraman wrote:
*Dear All,
Could anybody suggest me some books or notes or some
materials which will help me to understand the way gromacs algorithms
work i.e. how neighbor group search works e.t.c. I kindly request you to
suggest me other than the gromacs
Actually Mark, I may have made a very trivial error. Forget about it for
now.
Cheers
Gavin
Gavin Melaugh wrote:
Hi Mark
My Apologies. Here is more info.
gmxdump -f traj.trr history
From history I take the coordinates at 250 ps and convert to gro file
say test.gro
trjconv -f traj.trr
Ben Ahmady wrote:
Dear GROMACS users/developers
I've recently started a PhD and am currently looking at bilayer
formation of two-tailed alkyl phosphate esters. I've been using the
PRODRG server to generate topologies for use in GROMACS, and as per the
recommendations made in the paper by
Dear All
I'd like to perfom a deuterium oerder parameters analysys in a system with DPPC
+ Protein + Water
I read that I've to make an index file that contains one group each for every
carbon atom in the acyl-chain (starting
with the carbonyl-carbon and going further down).
Where can I get
On Wed, Nov 2, 2011 at 2:06 PM, Alex alexbioi...@yahoo.com wrote:
Dear All
I'd like to perfom a deuterium oerder parameters analysys in a system with
DPPC
+ Protein + Water
I read that I've to make an index file that contains one group each for
every
carbon atom in the acyl-chain
Dear Justin
Parameterization is a tough task, if done properly. If you find it
came easy, it's probably not right ;) It sounds like you're trying to
work backwards from PRODRG and correct the charges. While that can be
OK, if you've committed to using the Gromos96 force fields, I'd
suggest
Hi Justin and Mark,
Thank you so much for your replies. Mark, would you mind clarifying what
you mean? What exactly should I be looking for in the ffbonded.itp file?
I'm not sure why those bonded parameters in particular were overridden... I
didn't intend to modify anything!
Perhaps it would
On 02.11.2011 13:38, Ravi Kumar Venkatraman wrote:
Could anybody suggest me some books or notes or some
materials which will help me to understand the way gromacs algorithms work
i.e. how neighbor group search works e.t.c. I kindly request you to suggest
me other than the gromacs manual.*
Dear Gromacs Users,
I am simulating a system where monomers interact via both bonded and nonbonded
potentials. My data analysis includes computing elements of the pressure
tensor. Is there a way to distinguish contributions of the non-bonded forces
from those of the bonded forces when
Dear all,
I've trying to run a simulation on a IBM Power6 cluster. At the
beginning of the simulation I've got a segmentation fault. I investigated with
TotalView and I've found that this segmentation violation originates in the
pwr6kernel310.F
Up to now, I still didn't find what is behind this
Ben Ahmady wrote:
Dear Justin
Parameterization is a tough task, if done properly. If you find it
came easy, it's probably not right ;) It sounds like you're trying to
work backwards from PRODRG and correct the charges. While that can be
OK, if you've committed to using the Gromos96 force
Olivia Waring wrote:
Hi Justin and Mark,
Thank you so much for your replies. Mark, would you mind clarifying what
you mean? What exactly should I be looking for in the ffbonded.itp file?
I'm not sure why those bonded parameters in particular were
overridden... I didn't intend to modify
Olivia Waring wrote:
Yes, it's the same error.
About the bond types: should they be defined as opls_* in ffbonded.itp,
aminoacids.rtp, both, or somewhere else entirely?
The bonds are named in the aminoacids.rtp file, they are defined in
ffbonded.itp. Use names in the .rtp, types in
On 3/11/2011 12:21 PM, cuong nguyen wrote:
Dear,
I have used JME in PRODRG to draw acid hexanoic molocule. However,
after running, the H atom in -OH could not be created and two oxygen
atom were the same.
Please tell me what are the errors?
This mailing list is for GROMACS-related
cuong nguyen wrote:
Dear,
I have used JME in PRODRG to draw acid hexanoic molocule. However, after
running, the H atom in -OH could not be created and two oxygen atom were
the same.
Please tell me what are the errors?
Please read the PRODRG FAQ's, where protonation state is addressed.
Dear users:
does anybody know where the OPLS magnesium parameters are from? As far
as I can tell, they are not in Jorgensen 1996 or Kaminski 2001, In
spite of the fact that many simulation studies reference these papers
for their magnesium opls parameters.
In fact, I do not think that
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