On 15/12/2011 5:59 PM, mohammad agha wrote:
Dear Prof.
May I ask you two questions, Please?
1- I work with MARTINI force field. I have a surfactant molecule
consists of 5 beads. After I placed 151 surfactants into my simulation
box (cubic) with length of 10 nm, Gromacs reported:
Volume = 100
Dear Prof.
May I ask you two questions, Please?
1- I work with MARTINI force field. I have a surfactant molecule consists of 5
beads. After I placed 151 surfactants into my simulation box (cubic) with
length of 10 nm, Gromacs reported:
Volume = 1000 nm3
Density = 15.8111 gr/l
My volume is right
Hi Mark,
Thank you very much for your help. I got my answer.
I chose protein as the group for calculating SASA and residue1 for output
and i got the SASA of residue 1 vs time. This gave me the correct mean SASA
of residue1 and also its std deviation.
I repeated the same way for all the residues
On 15/12/2011 4:51 PM, aiswarya pawar wrote:
Hi,
When i tried running mdrun without mip i received the same error ie
when i gave mdrun -deffnm md
i got=
Back Off! I just backed up md.log to ./#md.log.1#
Getting Loaded...
Reading file md.tpr, VERSION 4.5.4 (single precision)
Loaded with Money
Hi,
When i tried running mdrun without mip i received the same error ie
when i gave mdrun -deffnm md
i got=
Back Off! I just backed up md.log to ./#md.log.1#
Getting Loaded...
Reading file md.tpr, VERSION 4.5.4 (single precision)
Loaded with Money
p0_23443: p4_error: interrupt SIGx: 4
Thank
On 15/12/2011 1:05 PM, ??? wrote:
Dear gromacs users
I used Gromacs in order to get a MD simulation of
Glycoproteion.now I have got the Glycoproteion's PDB file,When I want
to MD by GMX,it gave a Warnning:Fatal error: Residue ""not found
in residue topology database.
So check out
h
Thank your advance
I have check the residue names, in glyco parts, it
contain:NLN,2MA,6MA,WMB,4YB,0YB,XMA,0MA and so on.and I found the define of the
residue ,but the format of the define isn't adopt to the Gromacs 's .rtp file.
now I don't know how to do it, who can help me? thanking
2011/12/14 陈应广 <525342...@qq.com>
>
> **
>
>
> Dear gromacs users
>
> I used Gromacs in order to get a MD simulation of Glycoproteion.now I
> have got the Glycoproteion's PDB file,When I want to MD by GMX,it gave a
> Warnning:Fatal error: Residue ""not found in residue topology database.
Dear gromacs users
I used Gromacs in order to get a MD simulation of Glycoproteion.now I
have got the Glycoproteion's PDB file,When I want to MD by GMX,it gave a
Warnning:Fatal error: Residue ""not found in residue topology database. And
I know it was because of the force field,I wa
Dear all I am interested in simulating a model of Glycoproteion. I could'nt
find the define of the residue in any forcefield .rtp file of GMX. I am using
Gromacs 4.5.5 . If any one can help me in getting forcefield parameters for
charmm27/ OPLS/Amber99 in gromacs format please respond. Please s
Dear gromacs users
I used Gromacs in order to get a MD simulation of Glycoproteion.now I
have got the Glycoproteion's PDB file,When I want to MD by GMX,it gave a
Warnning:Fatal error: Residue ""not found in residue topology database. And
I know it was because of the force field,I wa
On 15/12/11, Yun Shi wrote:
> Hi Mark,
>
> I do not quite understand. For example, in amber ff, 1-4 interactions (except
> the part from dihedral interactions) are calculated according to non-bonded
> parameters and then scaled by 1/2 or 5/6.
Yes, see discussion of gen-pairs in manual s
Hi Mark,
I do not quite understand. For example, in amber ff, 1-4 interactions
(except the part from dihedral interactions) are calculated according to
non-bonded parameters and then scaled by 1/2 or 5/6. When setting nrexcl =
3, which is the default, aren't 1 - 4 interactions excluded from using
On 15/12/11, 李浩 wrote:
>
>
>
>
>
>
>
>
>
>
>
> dear users:
>
>
>
>
>
> I am using Gromacs 4.0.5. My system consist of chared plain and charged
> protein.
>
>
> How can i use the g_dipoles to get the protein's dipole? what is the exact
> option?
>
>
>
Start with g_di
On 15/12/11, lq z wrote:
> Dear GMXers,
>
> I need to use charmm ff (same question for amber ffs), and am confused with
> what value I should give to nrexcl in [ moleculetype ], 2 or 3?
Whatever value pdb2gmx generates for CHARMM, probably 3.
>
>
> According to the manual (v 4.5),
neeru sharma wrote:
Dear Gromacs users,
I have to simulate a system consisting of Protein+MG+GDP where Protein
is in complex with MG and GDP. I generated the GDP parameters using
antechamber and then converted the topology,coordinate and parameter
files to the corresponding gromacs format.
Dear Gromacs users,
I have to simulate a system consisting of Protein+MG+GDP where Protein is
in complex with MG and GDP. I generated the GDP parameters using
antechamber and then converted the topology,coordinate and parameter files
to the corresponding gromacs format.
Then, I tried to start with
Am using mipch2-1.2.7. Is this the problem?
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
-Original Message-
From: aiswarya.pa...@gmail.com
Date: Wed, 14 Dec 2011 13:09:19
To: Gromacs mail
Reply-To: aiswarya.pa...@gmail.com
Subject: Re: [gmx-users] submi
dear users:
I am using Gromacs 4.0.5. My system consist of chared plain and charged
protein.
How can i use the g_dipoles to get the protein's dipole? what is the exact
option?
Thanks!
Lee
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo
Dear GMXers,
I need to use charmm ff (same question for amber ffs), and am confused with
what value I should give to nrexcl in [ moleculetype ], 2 or 3?
According to the manual (v 4.5), "nrexcl = 3 stands for excluding
non-bonded interactions between atoms that are no further than 3 bonds
away."
shahid nayeem wrote:
Dear all
I am interested in simulating a model protein with cobalt forming
coordinate bond with His. I coud'nt find entry for cobalt in any
forcefield .rtp file. I am using Gromacs 4.5.4 . If any one can help me
in getting forcefield parameters for charmm27/ OPLSaa/Amber
Hi Carla,
> during my simulation, the dimer I'm simulating changed a lot.
> So when I calculate with g_rms, the RMSD between my initial and my final
> structure (choosing "Protein-H"), I get a value of 10 angstroms.
Have you made sure there are no atoms jumping across the boundaries?
> g_rmsf -s
Dear all
I am interested in simulating a model protein with cobalt forming
coordinate bond with His. I coud'nt find entry for cobalt in any forcefield
.rtp file. I am using Gromacs 4.5.4 . If any one can help me in getting
forcefield parameters for charmm27/ OPLSaa/Amber99 in gromacs format please
Hi everyone,
please I have a litle problem:
during my simulation, the dimer I'm simulating changed a lot.
So when I calculate with g_rms, the RMSD between my initial and my final
structure (choosing "Protein-H"), I get a value of 10 angstroms.
However, when I try to calculate a RMSDeviation aver
aiswarya.pa...@gmail.com wrote:
Mark,
I still the same error.
Check the .log file for any errors, and if you find none, then the problem isn't
from Gromacs and should be investigated with your sysadmin.
-Justin
Thanks
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Networ
Mark,
I still the same error.
Thanks
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
-Original Message-
From: Mark Abraham
Sender: gmx-users-boun...@gromacs.org
Date: Wed, 14 Dec 2011 23:03:59
To: Discussion list for GROMACS users
Reply-To: Discussion l
neeru sharma wrote:
Thanks Justin.
I have tried both ways now and considering Protein_MG_GDP and Water_ions
groups, it is running without any error but Protein_GDP and
MG_Water_ions is failing with an error message.
Well, without knowing the exact error message and all the steps you did
On 14/12/2011 11:20 PM, Linder Tobias wrote:
Dear gromacs users,
I used g_covar in order to get the eigenvectors of a MD simulation. Analysis of
the eigenvalue plot showed the high eigenvalue of the first eigenvector. I also
used gmxdump in order to analyse eigenvec.trr. Frame 1 of the eigenve
Dear gromacs users,
I used g_covar in order to get the eigenvectors of a MD simulation. Analysis of
the eigenvalue plot showed the high eigenvalue of the first eigenvector. I also
used gmxdump in order to analyse eigenvec.trr. Frame 1 of the eigenvec.trr
shows the eigenvector direction of each
Dear gromacs users,
I used g_covar in order to get the eigenvectors of a MD simulation. Analysis of
the eigenvalue plot showed the high eigenvalue of the first eigenvector. I also
used gmxdump in order to analyse eigenvec.trr. Frame 1 of the eigenvec.trr
shows the eigenvector direction of each
On 14/12/2011 10:30 PM, aiswarya pawar wrote:
Hi users,
I have a submission script for gromacs mdrun to be used on IBM
cluster, but i get an error while running it. the script goes like this=
#!/bin/sh
# @ error = job1.$(Host).$(Cluster).$(Process).err
# @ output = job1.$(Host).$(Cluster).
Hi users,
I have a submission script for gromacs mdrun to be used on IBM cluster, but
i get an error while running it. the script goes like this=
#!/bin/sh
# @ error = job1.$(Host).$(Cluster).$(Process).err
# @ output = job1.$(Host).$(Cluster).$(Process).out
# @ class = ptask32
# @ job_type =
Thanks Justin.
I have tried both ways now and considering Protein_MG_GDP and Water_ions
groups, it is running without any error but Protein_GDP and MG_Water_ions
is failing with an error message.
Thanks again...
Neeru
>
> neeru sharma wrote:
> >
> >
> > Thanks Justin.
> >
> > I tried the s
Hey :)
This is pretty incorrect... A high cosine content is an indicator of
unidirectional motion in phase space. I've elaborated on that on this
list some while ago.
> Regarding your case, this means that, even if the RMSD is stable starting
> from 5ns, the protein still experiences "random" mot
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