Dear justin
http://rmsdnagasundaram.blogspot.in/. This is the link to
my rmsd graph. Plz check it once and suggest me.
Thanks
On Mon, Sep 24, 2012 at 10:10 PM, ahmet yıldırım ahmedo...@gmail.comwrote:
Dear Tsjerk,
You said RMSD's above 1 nm are suspect, towards 2 highly
It looks for me like the known pbc effect others already pointed to. If
you have just a protein-ligand complex (+ water and counterions of
course) it's relatively easy to manually (a piece of code would do it)
bring the ligand to the correct position in the frames showing an
abnormally high
Dear Felipe
Thanks for ur reply.
The system is a protein-protein complex. Like u r saying its due
to pbc problem then why any abnormality doesn't happened to the native
complex (Black line)?. As already suggest by justin i checked the pbc
conditions upto my knowledge
On 09/25/2012 10:08 AM, naga sundar wrote:
Dear Felipe
Thanks for ur reply.
The system is a protein-protein complex. Like u r saying its due
to pbc problem then why any abnormality doesn't happened to the native
complex (Black line)?.
Maybe because MD is stochastic
On Tue, Sep 25, 2012 at 11:57 AM, Nur Syafiqah Abdul Ghani
pqah...@gmail.com wrote:
Dear All,
I already produce my co-solvent topology file also with gro file.
Next step is i need to put the co-solvent first before i enter the
water molecule inside my box and mix them with the protein.
But
Hi,
Your RMSD graph is ok but is represented wrong due to pbc problem. Use
whole and nojump options of trjconv.
On Tue, Sep 25, 2012 at 2:15 PM, Felipe Pineda, PhD
luis.pinedadecas...@lnu.se wrote:
On 09/25/2012 10:08 AM, naga sundar wrote:
Dear Felipe
Thanks for ur
Hi,
trjconv -s top.tpr -f traj.xtc -o traj-nojump.xtc -pbc nojump
I hope it helps
2012/9/25 Archana Sonawani ask.arch...@gmail.com
Hi,
Your RMSD graph is ok but is represented wrong due to pbc problem. Use
whole and nojump options of trjconv.
On Tue, Sep 25, 2012 at 2:15 PM, Felipe
Hi all,
I want to build elastic network model using gromacs. I consider
only c-alpha atoms and only bond stretching term contributes to towards
potential energy. Bonds are connected between atoms present with in
certain cut-off distance(modified topology accordingly). When I run md
Hi everyone,
This message is just to let people know that there is finally a
reference that we ask you to cite if you publish work using the CHARMM36
lipid force field contribution available from the GROMACS website. The
reference is provided in a new version of the forcefield.doc file, and
Hi,
I am a newbie in Gromacs and is trying to simulate a small organic
molecule in water. I got the following error message during a position
restrained md run. I tried changing number of nodes but without success.
Any help on this is appreciated.
Initializing Domain Decomposition on 16
On 9/25/12 12:20 PM, Dipankar Roy wrote:
Hi,
I am a newbie in Gromacs and is trying to simulate a small organic
molecule in water. I got the following error message during a position
restrained md run. I tried changing number of nodes but without success.
Any help on this is appreciated.
On 9/25/12 11:15 AM, Ali Alizadeh wrote:
Dear All users
I made a box of water molecules(w.pdb to w.gro by pdb2gmx then i
used genbox for made a box), but the grompp did not identify
molecules(water mode SPC),
error:
atom 5721 in wbox.top does not match with in wbox.gro
atom 5722 in
Dear all,
i am trying to convert a .gro file into a top file using .x2top but not all
atoms can be assigned forcefields and the code stops with the error:
Generating bonds from distances...atom 94Can not find forcefield for atom C-2
with 2 bondsCan not find forcefield for atom S-3 with 0
On 9/25/12 4:28 PM, Elie M wrote:
Dear all,
i am trying to convert a .gro file into a top file using .x2top but not all
atoms can be assigned forcefields and the code stops with the error:
Generating bonds from distances...atom 94Can not find forcefield for atom C-2
with 2 bondsCan not find
Thanks for your reply. I guess either way (x2top or pdb2gmx), I have problems.
pdb2gmx is giving the same old error residue 'UNK' is not found in topology
residue file whereas strangely enough x2top did not complain and was able to
assign topologies for 73 atoms out of 94 so maybe it is
On 9/25/12 5:02 PM, Elie M wrote:
Thanks for your reply. I guess either way (x2top or pdb2gmx), I have problems.
pdb2gmx is giving the same old error residue 'UNK' is not found in topology
residue file whereas strangely enough x2top did not complain and was able to
assign topologies for
Hi everyone,
This is probably a very silly question, but if I want to restrain only certain
lipid residues in my bilayer, based on their residue number, is there some
other way to do this aside from just having an explicit residue-by-residue list
of them their topologies in my .top? I'm just
Yep You are right. I will try my best to change the files accordingly.
Thanks
Date: Tue, 25 Sep 2012 17:05:20 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] error with x2top.
On 9/25/12 5:02 PM, Elie M wrote:
Thanks for your reply. I guess either
On 9/25/12 5:14 PM, Katrina Lexa wrote:
Hi everyone,
This is probably a very silly question, but if I want to restrain only certain lipid
residues in my bilayer, based on their residue number, is there some other way to do this
aside from just having an explicit residue-by-residue list of
Check to see if the MPICC and MPI_HOME environment variables are set
correctly to configure (it can't find mpicc).
On 2012-09-25 12:06:14PM -0300, Diego Nolasco wrote:
Hello GROMACS users,
I am facing some problems to configure the gromacs installation in a x86_64
GNU/Linux SGI Cluster XE
Sorry one more thing: For one of the atoms S that x2top did not assign the
topology it said 0 bonds although S is a part of the Thiophene molecule which
is connected to two carbons..what does it mean 0 bonds?
Thanks
From: elie.mouj...@hotmail.co.uk
To: gmx-users@gromacs.org
Subject: RE:
On 9/25/12 5:20 PM, Elie M wrote:
Sorry one more thing: For one of the atoms S that x2top did not assign the topology it
said 0 bonds although S is a part of the Thiophene molecule which is connected to two
carbons..what does it mean 0 bonds?
It means there is no entry in the .n2t file
That's a simple enough way to deal with it - thanks!
On Sep 25, 2012, at 2:16 PM, Justin Lemkul wrote:
On 9/25/12 5:14 PM, Katrina Lexa wrote:
Hi everyone,
This is probably a very silly question, but if I want to restrain only
certain lipid residues in my bilayer, based on their
Hi,
In my system, I have several hydroxyl groups. I would like to change the
hydroxyl hydrogens to deuterium (as an approximation, I will just double the
typical hydrogen mass). I am only doing this as a test of the dependance on
mass of my system, so while I am sure force fields involving
On 9/25/12 5:42 PM, Andrew DeYoung wrote:
Hi,
In my system, I have several hydroxyl groups. I would like to change the
hydroxyl hydrogens to deuterium (as an approximation, I will just double the
typical hydrogen mass). I am only doing this as a test of the dependance on
mass of my system,
Hi,
If you have time, I have one more question. Suppose that I have some atom
type named XX. Normally XX has a partial charge, but for a test simulation,
I would like to turn off the charges of all of the XX atoms. This way, I
will hopefully be able to disentangle the relative effects of
On 9/25/12 5:54 PM, Andrew DeYoung wrote:
Hi,
If you have time, I have one more question. Suppose that I have some atom
type named XX. Normally XX has a partial charge, but for a test simulation,
I would like to turn off the charges of all of the XX atoms. This way, I
will hopefully be
Justin,
Thank you for the reminder! I can't believe I forgot that important fact
about ffnonbonded.itp, but I did.
Andrew DeYoung
Carnegie Mellon University
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