Dear GROMACS users,I went through the mailing list but I am still not sure about my problem. I am going to simulate two chains in a tube using GROMACS. The chains are modeled as strings of connected beads and I would like to describe the interaction with the tube aligned with z axis and passing thr
Dear GROMACS users,my system is composed of a repulsive surface with chains grafted on it and other free chains above this immobilized system. I am hesitating whether to use dispersion corrections for the pressure and energy or not. Without these corrections the repulsion of the grafting surface in
Benkova wrote:Hello Justin, I was using cubic boxes. GreetingsZuzanaOn 02/15/11, Erik Marklund wrote:Justin A. Lemkul skrev 2011-02-09 23.03:>>>Zuzana Benkova wrote:>>Dear GROMACS users,>>>>I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds in water
Hello Justin, I was using cubic boxes. GreetingsZuzanaOn 02/15/11, Erik Marklund wrote:Justin A. Lemkul skrev 2011-02-09 23.03:>>>Zuzana Benkova wrote:>>Dear GROMACS users,>>>>I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds in water. I got t
Dear GROMACS users,I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds in water. I got the average number per time frame and number of water oxygen atoms equal to 0.839. When I used g_hbond of version 4.0.7 I got 1.677, which is twice the former value. TIP3P model predicts ove
Dear GROMACS users,I would like to run some simulations of systems combined of polyethylene oxide brushes and short homooligopeptides (alanine, 12 residues) using CHARMM force field with GROAMCS 4.0.5 version. I have used parameters from the CHARMM force field files from the newest version of GROMA
have tried that and if that helps at all, but also they are using a different simulation package.I am getting good rdf values for the water even with slightly low density, so I guess it is okay.ThanksQuoting Zuzana Benkova :>Hi Nisha,>>I have performed a benchmark simulations of TIP3P wa
Hi Nisha,I have performed a benchmark simulations of TIP3P water and I still obtained density 0.984g.cm-3. It looks that this model gives such a density. If you look at JCP 79, 926, 1983 you will see that the authors got 0.982g.cm-3 with MC. (Table 3) Try to evaluate alsoo other properties, each mo
, Zuzana Benkova <zuzana.benk...@savba.sk> wrote:
Dear GROMACS users,I have checked the mails in archive which deal with the problem I am facing but did not find the answer what I do wrong.
I want to compile a PEO chain centered in box of 2900 water molecules. In my md.mdp the relevant sect
Dear GROMACS users,
I have checked the mails in archive which deal with the problem I am
facing but did not find the answer what I do wrong.
I want to compile a PEO chain centered in box of 2900 water molecules.
In my md.mdp the relevant section is as follows
Tcoupl = nose-hoover
constructing according to the required format. I aslo compared it with other gro files, that worked. After replacing replacing of zero .0 by 0.0 the procesing was successful. Thank you for hint.ZuzanaDňa 03/04/10, Mark Abraham napísal:On 5/03/2010 4:08 AM, Zuzana Benkova wrote:>Dear GROMACS users
Dear Mark,I have used version 4.0.3.ZuzanaDňa 03/04/10, Mark Abraham napísal:On 5/03/2010 4:08 AM, Zuzana Benkova wrote:>Dear GROMACS users,>I wanted to do a test calculation on a linear unrealistic molecule PPPBC>without any contributions to energy exept of LJ nonbenoded interaction
Dear GROMACS users,
I wanted to do a test calculation on a linear unrealistic molecule
PPPBC without any contributions to energy exept of LJ nonbenoded
interactions. I have prepared a topol.top file which I am attaching.
After processing this file with grompp I obtained a message
WARNING 1 [file t
Dear GROMACS users,I wanted to do a test calculation on a linear unrealistic molecule PPPBC without any contributions to energy exept of LJ nonbenoded interactions. I have prepared a topol.top file which I am sending. After processing this file with grompp I obtained a messageWARNING 1 [file topol.
tually, so if you're not getting what you expect, provide the information I asked for above and hopefully someone should be able to figure out what's going wrong.-Justin>Zuzana Benkova>-- Justin A. LemkulPh.D. CandidateICTAS Doctoral ScholarMILES-IGERT T
Dear GROMACS users, I have a system of 64 chains and want to calculate averaged values of end-to-end distance of all chains as well as the averaged radius of gyration from 1ns trajectory. In the case of end-to-end distance I have prepared index file containing one group of the first atoms in ascend
is not possible. Could you be so kind and confirm my opinion that if I want to mix BH and LJ potential I have to define all interactions by tables. Zuzana Benkova
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Dear GROMACS users,
most likely I am asking a trivial question but I need to be sure about it
for calculations of heat capacity based on the fluctuations of energy in
canonical ensemble. I am doing simulation of water using TIP4P model. I
compare two systems consisting of 216 and 8*216 = 1728 mole
Dear GROMACS users,
I want to use GROMOS force field for the polyethylene simulations to compare
the performance of this force field with those generated for alkanes. I have
prepared my own files based on the ffG53a5 files. In itp I used
[ defaults ]
; nbfunccomb-rule gen-pairs
ould figure out that they give the wrong free energy of
hydration. I hope to have the parameters ready before the end of the
year. Meanwhile, you can use the recently optimized parameters for
CHARMM (http://dx.doi.org/10.1529/biophysj.108.133025) though they are
all-atom.
Cheers,
Patrick
Z
Dear GROMACS users
I want to run simulations of polyethyleneoxide melt. In literature I have
found united atoms force fields that performed well for this kind of
simulation. For dihedral potential I need to extend the Ryckaert-Bellemans
potential up to the order of six. I have looked at the mailin
Dear Chansoo Kim,
It has passed relatively long time since I attempted to use pdb2gmx to build
my topology for polyethylene. I prepared the relevant files according to
those used for amino acids. I used + and - sign to discern the direction of
connectivity. I have encountered dome problems mention
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Zuzana Benkova
Sent: Tuesday, November 04, 2008 3:11 PM
To: 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] running a simulation without production
Dear Mark,
Thank you very much fo
_
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Zuzana Benkova
Sent: Monday, November 03, 2008 5:49 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] running a simulation without production
Dear GROMACS users,
I want to simulate a system consisting of a
] [mailto:[EMAIL PROTECTED]
On Behalf Of Mark Abraham
Sent: Monday, November 03, 2008 9:55 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] running a simulation without production
Zuzana Benkova wrote:
> I have tried also running this job without user specified potential,
&g
Dear GROMACS users,
I want to simulate a system consisting of a plate modeled by atoms (5000
atoms) and a polyethylene chain (80 carbons). The plate is frozen and I am
using tabulated potentials. In this system, the considered interactions are
chain-chain and chain-plate. There are no electrost
Dear GMX users,
I want to analyse th ebond angle. I have used
mk_angndx -s md1.tpr -n angle.ndx
to prepare an index for g_angle.
After
g_angle -f md1.xtc -s md1.tpr -n angle.ndx
I have obtained
Software inconsistency error:
Not supported in get_stx_coordnum
Most likely this is a trivial q
Dear GMX users,
I want to analyse th ebond angle. I have used
mk_angndx -s md1.tpr -n angle.ndx
to prepare an index for g_angle.
After
g_angle -f md1.xtc -s md1.tpr -n angle.ndx
I have obtained
Software inconsistency error:
Not supported in get_stx_coordnum
Most likely this is a trivial que
Dear GMX users,
I want to prepare .gro and topology file starting from the .pdb file
for a polyethylene chain , whose residue is not defined in .rtp, .hdb.
and .tdb files. I have defined a new residue in ffoplsaa.rtp file as
follows
[ Eth ]
[ atoms ]
C1opls_136-0.1201
H1
Dear GMX users,
I want to prepare .gro and topology file starting from the .pdb file
for a polyethylene chain , whose residue is not defined in .rtp, .hdb.
and .tdb files. I have defined a new residue in ffoplsaa.rtp file as
follows
[ Eth ]
[ atoms ]
C1opls_136-0.1201
H1
Dear GMX users,
I want to prepare .gro and topology files starting from the .pdb file
for a polyethylene chain , whose residue is not defined in .rtp, .hdb.
and .tdb files. I have defined a new residue in ffoplsaa.rtp file as
follows
[ Eth ]
[ atoms ]
C1opls_136-0.1201
H
PROTECTED]
On Behalf Of Mark Abraham
Sent: Thursday, May 03, 2007 3:46 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Temperature increase
Zuzana Benkova wrote:
> I have run an NVE simulation of decamer of glycin first with PBC
> (coulombtype=Cut-off) and later witho
I have run an NVE simulation of decamer of glycin first with PBC
(coulombtype=Cut-off) and later without PBC (coulombtype=PME). The gen-temp
was set to 300K with option gen-vel=yes. The temperature start to raise
during simulation and finaly the following messages appeared in log file
Shake did no
test
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Hello gmx-users,
I have only little experiences with Gromacs and I am
trying to run MD simulations on polyethelenes. I tried to modify the
ffoplsaa.rtp and ffoplsaa.hdb where I have added my own residui. The addition
in ffoplsaa.rtp is as follows
; Ethyle - CH3-CH2 the first unit in po
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