On 12/14/12 12:40 PM, Dr. Vitaly Chaban wrote:
If you have a correct temperature for the particle of interest,
everything is correct.
One important caveat, of course, is a given thermostat's ability to produce
velocities that belong to a real NVT ensemble. This is not the case, for
instan
On 12/14/12 2:22 PM, Eduardo Oliveira wrote:
Hi,
I'm trying to use AMBER03 force field with my protein but when i run pdb2gmx i
get a fatal error message:
Fatal error:
Incomplete ring in HIS415
The problem is, when I open the structure on pymol i can't see any missing
atoms. Does anybody h
On 12/14/12 2:28 PM, James Starlight wrote:
Today I've tried to rename atoms from Swiss's params specific names to
the standard charmm names and obtain the set of the same errors
No default Improper Dih. types
No default U-B types
No default Bond types
Its strange to me because chromophore
On 12/14/12 3:20 PM, James Starlight wrote:
Justin,
in the case of the system with the atom types assigned from that paper
the grompp produced above 118 errors of non standard bond, angle as
well as dihedral types ;o So it' seems that some 118 addition terms
must be added to the ffbonded.itp t
On 12/14/12 11:42 PM, James Starlight wrote:
The topology with the below params produced that 118 errors during
grompp processings ( after pdb2gmx processing the geoetry of the
mollecule was correct )
[CRN]
[ atoms ]
CG2 CA-0.0900 0
CD1 CA-0.0800 1
CD2 CA-0.0800 2
CE1 CA-
;ve
done in accordance to that paper could you provide me with them for
comparison with my model ?
James
2012/12/14, Justin Lemkul :
On 12/14/12 3:20 PM, James Starlight wrote:
Justin,
in the case of the system with the atom types assigned from that paper
the grompp produced above 118 errors of
On 12/15/12 10:58 AM, John Doe wrote:
Hello All,
I was wondering if it's possible to print to a file different thermo data, such
as force on atoms, pressure, bond energies, ect?
Energy terms are stored in the .edr file and forces on atoms are stored in the
.trr file provided you set nstf
On 12/15/12 4:03 AM, mirc...@sjtu.edu.cn wrote:
Dear All:
I encountered a problem when doing umbrella sampling. The distance calculated
by grompp and g_dist is different, as shown by the following:
grompp z component of g_dist(since I am constraining the distance between two
groups along t
On 12/15/12 2:18 PM, James Starlight wrote:
So as I understood it've happened because the conformation of the
adjacent residue is differ when that residue bounded to the
chromophore ( in comparison to the residue in unbound capped form).
Conformation is irrelevant; atom types are all that ma
On 12/16/12 12:52 AM, James Starlight wrote:
Justin,
It's not quite understood for me why such errors occurs in the atoms
of standard residues when I've bounded them to the C term of my
chromophore if the geometry of the adjacent residues might not be
changed. So it likely that some errors occ
On 12/16/12 10:34 AM, James Starlight wrote:
Justin, thanks again for explanation.
So the first 5 atoms in cmap.it correspond to the starting sequence of
the backbone atoms of the amino acid doesnt it ? So what is the 24 24
numbers at the end of each cmap line ?
Probably something related t
On 12/16/12 1:11 PM, francesco oteri wrote:
Hi fatemeh,
thank you for the references. Regarding your problem, what does it means
you don't see any interaction?
Is it possible it is just a problem of the visualization software. To be
sure, you could monitor the distance
between any S atom and th
On 12/16/12 10:15 PM, Kieu Thu Nguyen wrote:
Dear All,
I am practising the tutorial 2 of Gromacs ( KALP-15 in DPPC). In the
step "Solvate
with water",i made a copy of vdwradii.dat and changed the value of C from
0.15 to 0.375. But i don't know how to input this changed file into genbox.
I saw
On 12/16/12 11:55 PM, Shine A wrote:
Sir,
I studying the dynamics of membrane proteins.First I did a 20 ns
simulation using GROMOS96 53a6.This force field cause some problems in the
helical part of the protein.Now I am trying to do the same simulation with
opls-aa force field.Is the chan
On 12/17/12 5:57 AM, ananyachatterjee wrote:
Dear all,
While running mdrun using following mdpparameters:
title= Model MD
; Run parameters
integrator= md
nsteps= 500
dt= 0.002
; Output control
nstxout= 500
nstvout= 500
nstxtcout= 500
nstene
On 12/17/12 8:53 AM, Kieu Thu Nguyen wrote:
Dear All,
I'm practising the tutorial 2a (protein in water) in the MARTINI tutorial.
After doing step 6 (Do a short energy minimization and position restrained
simulation),i carry out running NVT equilibrium. But it appears the error
in the terminal
On 12/17/12 8:55 AM, Eduardo Oliveira wrote:
Hi,
I'm setting my system but when I run grompp I get a warning and the program
terminates. It says the following:
You are using pressure coupling with absolute position restraints, this will
give artifacts. Use refcoord_scaling option.
I wan
On 12/17/12 9:06 AM, Eduardo Oliveira wrote:
OK, so if i got this right all I have to do is add another line in the mdp file
with refcoord_scaling = com? I thought that i had to make a substitution in one
of the existing terms.
Right, it's a new term entirely (see the manual). All keywords
starting structure, etc.
-Justin
On Mon, Dec 17, 2012 at 8:56 PM, Justin Lemkul wrote:
On 12/17/12 8:53 AM, Kieu Thu Nguyen wrote:
Dear All,
I'm practising the tutorial 2a (protein in water) in the MARTINI tutorial.
After doing step 6 (Do a short energy minimization and position restr
On 12/17/12 9:24 AM, Kieu Thu Nguyen wrote:
Dear All,
When i do the "Step Four: Adding Ions"in the tutorial "KALP-15 in DPPC", it
appears the error:
Fatal error:
No such moleculetype W
I checked .top file and included.itp files, they have definded water
molecule type name is "W".
What happe
On 12/17/12 11:38 AM, Kieu Thu Nguyen wrote:
Thank Justin ! I found my mistake. But when i type the next command line
genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname
CL -nn 4
and choose group 0 (system), the error is
Fatal error:
No line with moleculetype 'System'
On 12/17/12 12:53 PM, Shine A wrote:
sir,
I am studying dynamics of a membrane protein using oplsaa force field.
Energy minimization during nvt equilibration getting error like this.
Fatal error:
1 particles communicated to PME node 1 are more than 2/3 times the cut-off
out of the doma
On 12/17/12 1:48 PM, zugunder wrote:
Hi,
I want to simulate a water soluble protein of approx. 160aa size and its
shape from a .pdb looks a little elongated (if rotated around the longest
axis, it roughly occupies a cylinder with length to diameter ratio 1.8 -
1.9). Would it be considered glob
On 12/17/12 2:03 PM, Albert wrote:
well, that's one of the log files.
I've tried both
VERSION 4.6-dev-20121004-5d6c49d
VERSION 4.6-beta1
VERSION 4.6-beta2
and the latest 5.0 by git.
the problems are the same.:-(
It seems to me that the system is simply crashing like any other that beco
On 12/17/12 2:14 PM, zugunder wrote:
Thank you, Justin, for the prompt answer!
Justin Lemkul wrote
In almost all cases, a dodecahedral box is the optimal choice. A cubic
box with the same periodic distance for an elongated protein would be much
larger.
OK, got it.
Justin Lemkul wrote
On 12/17/12 3:04 PM, zugunder wrote:
Justin Lemkul wrote
It is calculated correctly, the math is just a bit more complex (see the
manual for the equations). The distance to the box edge is defined the
same way, but the two approaches don't necessarily give equally suitable
results. Con
On 12/17/12 4:01 PM, fatemeh ramezani wrote:
Dear Justin
According to papers, I expect gold atom interacts with the sulfur atom of amino
acid cysteine covalently. But in last email you said in the case of protein-Au
This will not be true to add these parameters
in topology file. Then
On 12/17/12 5:51 PM, Tom wrote:
Dear Gromacs Users,
I created a new residue on aminoacids.rtp file
and assigned improper dihedral after [ bonds ], for example
[ impropers ]
C2H C3 S1
Then I want to add the parameters of this dihedral angle potential
onto ffbonded.itp
I k
On 12/17/12 7:17 PM, Kieu Thu Nguyen wrote:
Dear All,
When i do step EM, the output file .gro is separated into many step.pdb
files . And many errors "Water molecule starting at atom XXX can not be
settled" appears. And the potential energy is positive !
What should i do to solve it ?
Pl
On 12/17/12 8:47 PM, Christopher Samuel wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On 17/12/12 21:57, ananyachatterjee wrote:
[ganga:04205] *** Process received signal *** [ganga:04205] Signal:
Segmentation fault (11) [ganga:04205] Signal code: Address not
mapped (1) [ganga:04205]
On 12/18/12 10:30 AM, Kieu Thu Nguyen wrote:
Dear All,
Are there any difference in nvt.mdp and npt.mdp files between MD-CG and
MD-AA ?
Settings in the .mdp file are dictated by the chosen force field. Every force
field is different and requires proper settings.
-Justin
--
=
On 12/18/12 1:22 PM, zugunder wrote:
Hi,
I have a general question on cutoff values.
I am using an AMBER03 ff and in a number of papers/tutorials the cutoffs for
vdw/coulomb are reported as low as 0.8 (and up to 1.2 - 1.4 depending on the
interaction type). As far as I understand, increasing t
On 12/18/12 1:29 PM, Yun Shi wrote:
Hi all,
I understand a suffix of "com" indicates center of mass, but how about
"cog" and the prefixes "whole" and "part"?
COG = center of geometry.
From g_select -select 'help all' you will find:
"3. POSTYPE of ATOM_EXPR calculates the specified positio
On 12/18/12 1:44 PM, zugunder wrote:
Justin Lemkul wrote
You need a .tpr file and can re-wrap the periodic image with trjconv -pbc
mol -ur compact.
Funny, it needs a file which I don't find:
g_trjconv -f nvt_minimized.trr -o nvt_minimized_compact.xtc -pbc mol -ur
compact
Program g_tr
On 12/18/12 2:02 PM, James Starlight wrote:
Dear Gromacs Users!
I'm looking for 150-200 lipid bilayer ( POPC or POPE) parametrized in
charmm27 or charmm36 force field and pre-equilibrated in NPT
conditions. I'll bevery thankfull to anybody who provide me with the
coordinates as well as itp fil
On 12/18/12 2:04 PM, zugunder wrote:
Justin Lemkul wrote
If you don't specify an actual file name to -s, then all Gromacs tools
look for a default file name, which in this case is "topol.tpr." Since
you've run a simulation, clearly you have a .tpr file, which is what yo
On 12/18/12 3:59 PM, XUEMING TANG wrote:
Hi there
I searched through the website for g_sans, which is a simple tool to
compute Small Angle Neutron Scattering spectra. But I cannot find it in
gromacs folder?
I found it in the following website:
http://gromacs.5086.n6.nabble.com/g-kinetics-g-op
On 12/18/12 9:47 PM, Nur Syafiqah Abdul Ghani wrote:
Dear Users,
Why I run the command genbox -cp protein_box.gro -ci hfi.gro -nmol
1534 -cs spc216.gro -p control.top -o protein_mixsol.gro.
And the result show like below.:
Grid: 15 x 15 x 11 cells
nri = 9466, nrj = 77062
Try 9579box_margin
On 12/19/12 6:02 AM, fatemeh ramezani wrote:
Dear Justin
I want exactly this, that the distance between Au-S be stable around
equilibrium value, For this purpose,Should I put the harmonic parameters
related to the gold and sulfur in ffbonded file? Or I should consider AU-S
connection as V
On 12/19/12 5:29 AM, Oliver Kuhn wrote:
Hi Gromacs People,
we want to do a BAR calculation to calculate the binding affinity change
induced by a mutation.
That means:
- We want to transform a residue from aminoacid1 (aa1) to aminoacid2 (aa2)
in a single-transformation approach (transforming b
On 12/19/12 4:12 AM, Nash, Anthony wrote:
Good morning,
A bit of a long one I am afraid.
I am simulating a transmembrane dimer, and calculating the association free
energy through potential of mean force calculations as a function of
interhelical distance. I have got very good umbrella cove
If the curves haven't stabilized, then you have a sampling problem, requiring
either more windows or longer time within each window.
-Justin
Many thanks
Anthony
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of
On 12/19/12 9:37 AM, Kavyashree M wrote:
Dear users,
While using g_hbond, does it make any difference if I give option
18 and 1 or 1 and 18?
Order does not matter.
I wanted to find the hydrogen bonding of a group of residues with
the whole protein so I had an index of this group. When I gi
On 12/19/12 11:43 AM, Kavyashree M wrote:
Sir,
I thought that the order should not matter but when I used 18 - 1
and 1 - 18 the graph were slightly off.
Group 18 is a set of residues in that protein with some unique property.
I wanted to see the variation of Hbond of these residues with the w
On 12/20/12 11:38 AM, Kieu Thu Nguyen wrote:
Dear All,
I convert cg to fg representation by command lines
g_fg2cg -pcg cg.top -pfg fg.top -c cg.gro -n 1 -o fg.grog_fg2cg -pcg
cg.top -pfg fg.top -c cg.xtc -n 1 -o cg2fg.xtc
But there is a notice "command not found" in the terminal.
I see thi
On 12/20/12 2:47 PM, zugunder wrote:
Could it be, say, because of still big conformational changes of the protein?
The size of the system is not that small: the protein is hydrated with 10921
water molecules.
Generally restraints are applied to the solute during equilibration to avoid
struc
On 12/21/12 12:55 PM, Alexey Shvetsov wrote:
Justin Lemkul писал 19-12-2012 01:10:
On 12/18/12 3:59 PM, XUEMING TANG wrote:
Hi there
I searched through the website for g_sans, which is a simple tool to
compute Small Angle Neutron Scattering spectra. But I cannot find it in
gromacs folder?
I
On 12/21/12 12:46 PM, zugunder wrote:
Justin Lemkul wrote
Depends on the algorithm. Pressure is a fickle metric (see
http://www.gromacs.org/Documentation/Terminology/Pressure and previous
discussions on this list). It is generally advisable to run equilibration
using weak coupling (i.e
On 12/21/12 2:57 PM, emmanuelle wrote:
Thanks for your reply.
1.My cutoffs are OK. Indeed, changing them leads to the same problem.
This outcome points to a topology or configuration issue.
2.My original box is 20nm in length. I generate it using genconf to avoid
any lack of memory that ge
On 12/23/12 3:21 AM, Davit Hakobyan wrote:
Dear Gromacs users,
I use Gromacs 4.5.1. The problem relates to the restarting procedure of a run. Usually I restart the run with
the "-append" option and now I need to move the ".trr" and ".xtc" files to
another directory since they got too big
On 12/24/12 7:38 AM, Wu Chaofu wrote:
Dear gmxers,
I want to recalculate potential energies for the frames generated
previously. At first, I generate one tpr file with a bit difference
from previous one used for generating those frames. Using this tpr
file, then I restart mdrun with -return opt
On 12/23/12 10:03 AM, IsaureCB wrote:
Dear gmx-users,
I would like to select, for each residue of a model, the residues that are
within 3.6 A in average over a simulation.
g_mdmat must create this information at some point while generating the
contact diagrams, but I would like to extract t
On 12/24/12 10:51 AM, sreelakshmi ramesh wrote:
Dear all,
I am trying repeat a work in which the system is coupled to the
Andersen thermostat in which they say they use a coupling constant p =
0.0003 .
could anyone of you tell me does it mean tau_t is 0.0003. Any help
apprecia
On 12/24/12 11:54 AM, Ankita naithani wrote:
Hi again,
Sorry for the repetition in email.
When I ran the mdrun command, I got an error of
"Attempting to read a checkpoint file of version 13 with code of version 12"
Can anyone please help me with this error too?
This means you are not usi
On 12/24/12 12:43 PM, Ankita naithani wrote:
Hi Justin,
Thank you so much for your response.
I also noticed that when I type in gmxcheck -f md.cpt to see which
version was used, I get the same fatal error of "Attempting to read a
checkpoint file of version 13 with code of version 12".
In my
On 12/24/12 5:53 PM, Steven Neumann wrote:
Dear Gmx Users,
I run pulling simulation of my ligand away from the protein. I
produced 1500 frames and run US windows with 0.1 nm spacing. However,
I have a gap in histograms - I need to use lower value of nstxtcout to
get the proper window where the
On 12/24/12 10:08 PM, Kieu Thu Nguyen wrote:
Dear All,
When i merge 2 file.gro by command "cat", the atom number have not updated
by itself.
Are there any method for this problem ?
Manual manipulation requires manual updating.
-Justin
--
Justin A
On 12/24/12 10:38 PM, Kieu Thu Nguyen wrote:
Sorry, i don't see where is manual for updating.
I don't mean the Gromacs manual, I mean "manual" in the sense that if you modify
a coordinate file without using one of the Gromacs tools, then you must manually
(i.e. by yourself using some extern
On 12/25/12 1:33 AM, Kieu Thu Nguyen wrote:
But i don't see file "gromacs_topology_merger.py" in the web Vedat gave me.
Tsjerk, can you give me the script for updating the number of atoms ? I
searched in google, but i have not found it yet. It's really my stupid
question, but i don't know why.
On 12/25/12 2:42 AM, Shima Arasteh wrote:
Hi all,
I'm trying to simulate a system of POPC- Protein- Water- Ion following the
Justin's tutorial of Kalp15-DPPC.
I get the system-solved-ion.gro and run energy minimization. I saw some water
molecules in em.gro file, therefore, I erase them a
On 12/25/12 3:51 AM, Steven Neumann wrote:
Maybe I wrote it wrote it wrong.
I have 1500 frames of which with 0.1 nm spacing I have chosen 14 to
run umbrella sampling windows.
I used:
conf0.gro
conf140.gro
conf213.gro
conf262.gro
conf263.gro
conf300.gro
...
conf1500.gro
However, the moment w
On 12/25/12 8:41 AM, Steven Neumann wrote:
Thank you Justin.
It is weird I cannot reproduce it with the same mdp:
title = Umbrella pulling simulation
define = -DPOSRES_T
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 15; 0.3 ns
nstcomm
On 12/25/12 8:53 AM, Steven Neumann wrote:
The other option would be to decrease force constant in two windows in
between of which is the gap. Then histograms for them willl be more
wide and they will overlap. Is that possible to combine windows using
WHAM with different force constants?
Yes
On 12/25/12 12:53 PM, Shima Arasteh wrote:
In order to compare the first and the second .gro file, I used grep -c OW
(file.gro) to see how many waters exist in my new system. I got 22352, however
I got 23703 before ( when I had not deleted the disturbing water molecules). So
23703-22352=13
On 12/25/12 5:45 PM, xiaowu759 wrote:
Dear gmxer's
I employed the same gro and mdp files but different top files (only excl is
different) for running previous and rerun mdrun with the generated frames.
As I realize, the the rerun mdrun seems to restart one completely new mdrun
which is not base
On 12/26/12 9:50 AM, vidhya sankar wrote:
Dear justin
Thank you for your Previous reply
I Have Successfully constructed topology for cyclic peptide using spce bond
and Other Appropriate Changes in the . top files
Yet I Want to make CO Terminal But When I interactively Choo
On 12/26/12 12:57 AM, Kavyashree M wrote:
Dear users,
I was using g_dih to find the phi/psi transitions of a protein
along the trajectory using the following command -
g_dih -f a.xtc -s a.tpr -o dihout.out -b x -e y -w
When it started running it indicated many of the following lines
"Dihedral a
On 12/26/12 6:32 PM, Gert Peters wrote:
Hi everybody,
Im trying to use GROMACS for MD of a RNA model generated by Rosetta (FARFAR).
As a test I try processing a modelledpdb file. When I prepare thetopology
files (pdb2gmx -f test.pdb -ff amber99 -ignh ) from pdb I encounter following
output :
On 12/26/12 7:46 PM, Kieu Thu Nguyen wrote:
Do you mean that i have to add the line "sed '2s/^.*$/'$(wc -l file.gro)'/'
file.gro > out.gro" into the old script merge.py ?
sed is a standard *nix command, issued from the command line.
-Justin
On Wed, Dec 26, 2012 at 6:39 PM, Tsjerk Wassena
On 12/28/12 2:24 AM, Shine A wrote:
sir,
I am studying the dynamics of membrane protein.I want to use amber force
field.Then what changes should I make in the ffnonbonded.itp and
ffbonded.itp?Is it similar as in Justin manual?Is it necessary to convert
C6 and C12 values in lipid.itp(for gro
On 12/27/12 8:44 PM, yeqing1211 wrote:
Hello everyone:
I prepar to make a QM/MM simulation by employing gromacs compiled
with mopac, and need to define two groups which are treated by QM and MM
separately, the question is this: during the dynamics course of my research
system, particles
On 12/29/12 7:03 AM, Shima Arasteh wrote:
Dear gmx users,
I want to delete some water molecules from .gro file. When I delete them, the
modified file is not readable and I can not visualize it anymore?
Would you please guide me how I can modify a gro file?
Update the second line of the f
The only way I can reproduce the error is by incorrectly executing GMXRC. If
one tries:
source /usr/local/gromacs/bin/GMXRC
it works just fine. If, from /usr/local/gromacs/bin, you directly run:
./GMXRC
you get the errors you quote below. The error indicates that you are not
correctly s
On 12/30/12 6:25 AM, Shima Arasteh wrote:
Hi,
If I get a fatal error of " water molecule can not be settled", where in log
file or bash I can find the disturbing water molecules? Would you please guide me? I
constantly get this fatal error! :-(
http://www.gromacs.org/Documentation/Errors#
On 12/30/12 12:28 PM, Nash, Anthony wrote:
Dear gmx users,
I posted a couple of weeks ago with regards to correctly using umbrella
sampling and the WHAM on atomistic transmembrane proteins with a reaction
coordinate as a function of interhelical distance. I have a single TM dimer,
but with a d
On 12/30/12 2:57 PM, Nash, Anthony wrote:
Dear Justin
Thanks for your reply.
I am studying a TM peptide, looking at how favourable the front and reverse
face are. Hence, different orientations but the same composition of amino
acids.
I then have a duplicate of this system (call it system B),
On 12/31/12 3:17 AM, Shima Arasteh wrote:
I know that I can use pdb and build my index file. But I want to know the
problem. What's the problem?
It sounds rather unbelievable that editconf would mysteriously delete atoms.
There is no way for anyone to say what is going on given the curr
On 12/31/12 11:20 AM, Shima Arasteh wrote:
No, I see CL ions in gro file after using editconf, but when I want to make an
index file, there is not CL option to choose!
What Gromacs version is this? I cannot reproduce this problem with 4.5.5 or the
development 4.6 version. Anything I have
On 12/31/12 11:45 AM, Shima Arasteh wrote:
It is 4.5.5.
I need to say that I had a pdb file which was produced by VMD, May it be the
reason of problem?
Without seeing the aforementioned information (substituting make_ndx screen
output for editconf command, which is not relevant), it's i
On 12/31/12 11:58 AM, Shima Arasteh wrote:
These are the last line of my gro file:
5SOLHW299818 7.429 8.372 11.524
5CL CL99819 0.485 3.864 11.451
5CL CL99820 5.689 6.730 9.692
9.21490 8.92980 12.40750
Here, I brought you the output of make_n
On 12/31/12 4:53 PM, Xu Dong Huang wrote:
Dear advanced gromacs users,
I have created an arbitrary molecule .gro file containing coordinates of my
martini-beads. basically, there are 50 beads sitting on each axis of (x,y, -x
and -y) forming like a cross. (Each bead with distance 0.43). Howev
en.rutgers.edu
On Dec 31, 2012, at 5:31 PM, Justin Lemkul wrote:
On 12/31/12 4:53 PM, Xu Dong Huang wrote:
Dear advanced gromacs users,
I have created an arbitrary molecule .gro file containing coordinates of my
martini-beads. basically, there are 50 beads sitting on each axis of (x,y, -x
a
On 12/31/12 5:50 PM, Xu Dong Huang wrote:
Dear Justin,
I'm pretty sure my .gro file is valid, here is a direct copy and paste of the
format of my .gro in the beginning:
star polymer
201
1starO41 0.000 0.000 0.000
1star O12 0.430 0.000 0.000
1s
On 12/31/12 5:50 PM, Xu Dong Huang wrote:
Dear Justin,
I'm pretty sure my .gro file is valid, here is a direct copy and paste of the
format of my .gro in the beginning:
star polymer
201
1starO41 0.000 0.000 0.000
1star O12 0.430 0.000 0.000
1s
On 12/31/12 9:41 PM, Xu Dong Huang wrote:
Dear Advanced Gromacs users,
I'm trying to generate a solvated system with >1 solute (In my case 3). I do
genbox -cp polymer.gro -nmol 2 -ci polymer.gro -cs water.gro -o polymer_solv.gro
-p polymer.top
My polymer molecule contains 201 atoms. box siz
On 1/1/13 8:56 AM, Shima Arasteh wrote:
Hi,
I have a system of Peptide-popc-ions-water to simulate. I'm trying to run MD
simulation following the Justin's tutorial of kalp15-DPPC.
The force field which I use, is charmm36.
In NVT step, I get LINCS-warning as follow:
Step 0, time 0 (ps) LINC
On 1/1/13 10:41 AM, Shima Arasteh wrote:
Thanks.
I compared settings of mdp files in POPC/WATER and POPC/PROTEIN/WATER systems. The only difference
I found between them was about the bonds constraints. The constraints of mdp file for POPC/WATER
was "constraints = h-bonds ", however it was "
On 1/1/13 10:53 AM, Shima Arasteh wrote:
If I tell you that I changed the constraints and now the NVT is running,
would that be ok? However I don't know the scientific reason of this incident!
But I bring you the EM.mdp as follow:
define = -DSTRONG_POSRES
integrator= steep
On 1/1/13 1:31 PM, Gert Peters wrote:
Dear all,
Im trying to run an md or em using an implicit solvation method using gromacs
4.5.5 but I allways get the same errors.
GB parameter(s) missing or negative for atom type 'OS'
GB parameter(s) missing or negative for atom type 'H2'
GB parameter(s
On 1/1/13 2:06 PM, Parisa Rahmani wrote:
Hi gmx users
I want to do secondary structure analyze for my trajectory of protein.
I've downloaded DSSP packages from "
ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4.tgz";
and put it in /usr/local/bin , and rename the folder to dssp.
when i run "do
On 1/1/13 2:01 PM, James Starlight wrote:
Have someone else any ideas how the topology for a simple 2D lattice
could be done ?:)
I've tried to build it manually but for the system of 48 nodes
definition of the angles and impropers have appeared very routinely :(
For regularly spaced atoms,
various properties of the different residues, so that's what you see it opening.
If there are no errors, it is running correctly. Failures are rather obvious by
design.
-Justin
On Tue, Jan 1, 2013 at 10:39 PM, Justin Lemkul wrote:
On 1/1/13 2:06 PM, Parisa Rahmani wrote:
Hi gmx use
On 1/1/13 10:33 PM, Xu Dong Huang wrote:
Dear advanced gromac users,
I am trying to simulate a long linear chain of polymer using CG beads. (about
200 beads), all with same type charge interactions. (examples shown:) I read on
previous gromacs mailing list that linear systems with same charg
On 1/1/13 10:46 PM, Xu Dong Huang wrote:
Dear Justin,
My .itp does not contain angles or dihedrals because we are simply interested
in the very simple generic case of a linear (what we assume by defining a
coordinate file of linear beads) polymer model. I will go through the tutorial
and tr
On 1/1/13 10:51 PM, Xu Dong Huang wrote:
@Justin,
Does the philosophy described in your tutorial apply to CG martini bead models
where 1 bead describes the entire CO2 atom? (If I were to do that, assuming)
Presumably. As long as you satisfy the criteria mentioned in the tutorial
(moment
On 1/1/13 11:48 PM, ramesh cheerla wrote:
Dear Gromacs users,
I am performing umbrella sampling
simulations by selecting configurations with spacing window of 0.02nm from
pulling simulations with the following options in .mdp file to get PMF
along a axis
On 1/2/13 4:36 AM, James Starlight wrote:
Justin,
I've already tried use g_x2top for the model of the system built from
regularly spaced C-atoms ( with included hydrogens to specify sp3
hybridization).
By means of that command I've created topology for my lattice with big
force constant ( fo
On 1/2/13 4:20 AM, Mijiddorj wrote:
I am a new user of Gromacs, I have problem with genbox. When I run genbox
following error occurred:Program genbox, VERSION 4.5.5Source code file:
/build/buildd/gromacs-4.5.5/src/gmxlib/futil.c, line: 491File input/output
error:/home/mijiddorj/Desktop/Tutorial
On 1/2/13 7:03 AM, Turgay Cakmak wrote:
Dear gromacs users,
I am trying to solvate several peptides (at a desired positions) in a
dodecahedron box. I have done following steps;
1) editconf -f peptides.gro -o peptides_nb.gro -c -d 1.0 -bt dodecahedron
2) genbox -cp peptides_nb.gro
On 1/2/13 7:15 AM, James Starlight wrote:
Justin,
so why my simulation of the sp3 lattice have been crashed with the
links warnings ( which always tells about wrong geometry in topology)?
Incorrect geometry is not the only cause of LINCS warnings. I haven't seen
nearly enough information
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