Dear users,
I have done simulation with my protein in water earlier successfully. Now, I am
trying to simulate protein in vacum similar to the last simulation of
protein-water. When I go to the NPT equilibration, I get a fatal error.
The commands I ran:
1.pdb2gmx -f monomer.pdb -o monomer.gro
Dear users,
I have done simulation with my protein in water earlier successfully using
CHARMM36 FF. Now, I am trying to simulate protein in vacum similar to the last
simulation of protein-water. When I go to the NPT equilibration, I get a fatal
error.
The commands I ran:
1.pdb2gmx -f
Dear users,
I have done simulation with my protein in water earlier successfully using
CHARMM36 FF. Now, I am trying to simulate protein in vacum similar to the last
simulation of protein-water. When I go to the NPT equilibration, I get a fatal
error.
The commands I ran:
1.pdb2gmx -f
There's nothing that leaps out at me as being wrong - but syntax checking
is the job of the parser (grompp) and logic checking can only be done by
you. To do that, I would proceed slowly, demonstrating that small chunks of
the force field can be used to generate results you can validate against
http://www.gromacs.org/Documentation/Terminology/Blowing_Up contains the
ideas that will likely help you, e.g. smaller time step, more
equilibration-friendly pressure coupling.
Mark
On Sun, Jan 27, 2013 at 1:59 PM, Shima Arasteh
shima_arasteh2...@yahoo.comwrote:
It is 15 ns of NPT
On 1/27/13 11:53 PM, Ewaru wrote:
Dear Gromacs experts,
I am running gromacs for the first time, and this is my em.mdp file.
define = -DFLEXIBLE
constraints = none
integrator = steep
dt = 0.01 ; ps !
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
On 1/28/13 2:45 AM, James Starlight wrote:
Dear Gromacs Users!
I'm simulating membrane receptor embedded in the explicit membrane
using charmm36 ff.
My simulation setup consist of
; Compound#mols
Protein 1
iso 1
POPC 228
SOL 11713
NA
On 1/28/13 4:47 AM, Shima Arasteh wrote:
Dear users,
I have done simulation with my protein in water earlier successfully using
CHARMM36 FF. Now, I am trying to simulate protein in vacum similar to the last
simulation of protein-water. When I go to the NPT equilibration, I get a fatal
Am I supposed to skip this step?
Thanks for your reply.
Sincerely,
Shima
___
From: Dr. Vitaly Chaban vvcha...@gmail.com
To: gmx-us...@gromuracs.org
Sent: Monday, January 28, 2013 3:17 PM
Subject: [gmx-users] Re: Protein in vacum
Dear users,
I have done
On 1/28/13 6:51 AM, Shima Arasteh wrote:
Am I supposed to skip this step?
Do not be tempted to think that there is a standard or required workflow.
The ensembles and environments you choose are dependent upon the task at hand.
There may be common workflows for proteins in water, but
YES.
On Mon, Jan 28, 2013 at 12:51 PM, Shima Arasteh
shima_arasteh2...@yahoo.com wrote:
Am I supposed to skip this step?
Thanks for your reply.
Sincerely,
Shima
___
From: Dr. Vitaly Chaban vvcha...@gmail.com
To: gmx-us...@gromuracs.org
Sent: Monday,
On 1/28/13 7:52 AM, Devika N T wrote:
Dear all
Can someone refer me a link to follow installation of gromacs 4.5.5 in
Fedora 15 ( fc15.x86_64)
http://www.gromacs.org/Documentation/Installation_Instructions_4.5
-Justin
--
Justin A. Lemkul, Ph.D.
Justin,
Below you can see graph representation of my system after energy
minimisation ( that case system was filled up with tip3p water using
genbox with slightly increased vdw for C atom ( to 2nm) to prevent
water movement into the membrane.
On 1/28/13 8:30 AM, James Starlight wrote:
Justin,
Below you can see graph representation of my system after energy
minimisation ( that case system was filled up with tip3p water using
genbox with slightly increased vdw for C atom ( to 2nm) to prevent
I'm assuming you mean 2 Angstrom?
Justin,
yes, 2 A for C atoms.
The dims are 8.68740 8.41864 10.0
James
2013/1/28 Justin Lemkul jalem...@vt.edu:
On 1/28/13 8:30 AM, James Starlight wrote:
Justin,
Below you can see graph representation of my system after energy
minimisation ( that case system was filled up with
On 1/28/13 8:45 AM, James Starlight wrote:
Justin,
yes, 2 A for C atoms.
The dims are 8.68740 8.41864 10.0
Well, with such a dramatic change, it should be fairly easy to simply watch the
trajectory and see what went wrong.
-Justin
--
On 1/28/13 9:30 AM, Sainitin Donakonda wrote:
Hello,
Recently i started working on molecular dynamics on my protein ligand
complex using gromacs i successfully did simulation but i dont know how to
visualize this protein-ligand complex this after MD simulation
Can any body tell me how to do
On 1/28/13 9:00 AM, Steven Neumann wrote:
Dear Gmx Users, Dear Justin,
I run umbrella samplig with small molecule binding protein. With 11
windows and 0.2 nm spacing I got:
PMF:
http://speedy.sh/zevcp/profile.JPG
Hisotogram:
http://speedy.sh/8Cua2/histo.JPG
(I used -min and -max options
Short answer is to inspect your complex with VMD or Pymol (or some
other viewer). Pymol takes pdb input, so unless your structure is
contained in a pdb file you must convert it with e.g. trjconv first.
If you want a single frame you need to extract one form your
trajectory, or, if the
I reduced time step in equi.mdp file to 20 ps. But the system is still not
balance. Should i continue reduce time step below 20 ps value ? Thanks so
much for any suggestion about appropriate time step value !
Regards,
KT
On Mon, Jan 28, 2013 at 12:53 PM, Kieu Thu Nguyen
On 1/28/13 10:02 AM, shahid nayeem wrote:
Dear Users
I am interested in knowing only the water molecules which remains
bounded to the protein during MD. Using g_select I can make a
boundwater.ndx file which gives water molecules within a specified
distance from the protein but it gives
On 1/28/13 10:29 AM, Kieu Thu Nguyen wrote:
I reduced time step in equi.mdp file to 20 ps. But the system is still not
balance. Should i continue reduce time step below 20 ps value ? Thanks so
much for any suggestion about appropriate time step value !
The first step I would take is to keep
Hi Justin
If I use the boundwaters.ndx to write another .ndx file using 1 2
3 4 and so on over all snapshots then also I should get the common
water molecules in these snapshots. Am I right.
Shahid
On Mon, Jan 28, 2013 at 9:03 PM, Justin Lemkul jalem...@vt.edu wrote:
On 1/28/13 10:02 AM,
On 1/28/13 10:53 AM, shahid nayeem wrote:
Hi Justin
If I use the boundwaters.ndx to write another .ndx file using 1 2
3 4 and so on over all snapshots then also I should get the common
water molecules in these snapshots. Am I right.
Presumably. Probably faster to try it and see rather
Dear users
I have 6 water molecules ,I want to constraint the distance between 6 oxygen
atoms in 0.42 nm from together.I read GROMACS manual but I had fatal erorr.
Here there is disres.itp file:
; Include Distance restraints file
#ifdef DDISRES
#endif
[ distance_restraints ]
;ai aj
On 1/28/13 2:10 PM, Masomeh Dehghani wrote:
Dear users
I have 6 water molecules ,I want to constraint the distance between 6 oxygen
atoms in 0.42 nm from together.I read GROMACS manual but I had fatal erorr.
Here there is disres.itp file:
; Include Distance restraints file
#ifdef
Dear all,
I am trying to calculate structure factor or scattering density of a
polymer in solution. The only tool I know is g_rdf -f .trr -s tpr. -sq -n
index
I provide an index file with System, Polymer (atom numbers of all polymers)
and Solvent (all solvent molecules) groups.
-startq
Hello,
В письме от 28 января 2013 16:06:20 пользователь Juliette N. написал:
Dear all,
I am trying to calculate structure factor or scattering density of a
polymer in solution. The only tool I know is g_rdf -f .trr -s tpr. -sq -n
index
g_rdf can calculate SAXS structurefactor
g_sans can
Its intresting that on the same system which was equilibrated longer
the decrease on the Z dim was smaller (from 10 to 9nm). By the way
does it possible to simulate membrane proteins (with explicit
membrane) in the nvt enssemble without explicit barostat ? What
options in the mdp should be added
Dear Gromac's users!
I have long trajectory with small intervals between individual
time-steps. Using editconf I'd like:
1- To extract last frame in pdb from my trajectory
(e.g for extraction of the first frame I'm using but its not working
with -dump -1 )
2- To convert my trajectory into xtc
Dear sir,
i have successfully created .gro file after neccessary correction
made in .rtp file. In the grompp_d comment, i am facing following errror.
could how can i rectify this error.
my comment is ./grompp_d -f em.mdp -c abnic2.gro -p abnic.top -o
abnic2.tpr
WARNING 1 [file
Hello Subramaniam,
For Unknown left-hand 'coloumbtype' in parameter file
There is type in you em.mdp file. Hence, change 'coloumbtype' to the correct
spelling 'rcoulomb'
The errors are generated as you are using non default bond types in your
'abnic_Other.itp' so check the bond type in
One important point:
in that simulations I've used decreased cut-offs with charmm36 ff
because that systems have been modelled with CPU+GPU so I had some
imbalance in cpu\gpu loadings with common (1.2) cutoffs.
rlist = 0.8 ; Cut-off for making neighbor list (short range
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