Hi!
What percent error is calculated as standard error by gmx analyze? 5%?
Thank you in advance and regards,
Raag
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Hi!
The gro file lost the data about the chains and treated the entire
heterodimer as one chain.
Anyway, problem solved! I checked the atom numbers from the gro file and
selected those in VMD. A bit tedious, but worked!
Thank you and regards,
Raag
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Hi!
I simulated a heterodimer and converted the md.gro file into a pdb file.
This pdb file I visualised in vmd. I wish to select residues (first 50,
then next 50 and so on), so that I can correlate the structure with the
graphs obtained by structure analysis.
If I give the command resid 1 to 50 an
Hi! This is not really a gromacs question, but I was wondering if you could
help, please!
I have a multiple line plot with a major difference between one of the
plots and the rest. Hence, I need to insert a gap in the y axis. I usually
use grace to plot the graphs generated by gromacs, but I’m una
I gave the following commands:
gmx_mpi trjconv -s md.tpr -f md.xtc -o md_noPBC.xtc -pbc mol -center (I
first selected 0 and then 1, like in the lysoyme tutorial).
gmx_mpi dipoles -f md_noPBC.xtc -s md.tpr
Despite that, I am getting opposite values in Mtot and aver. By re-center
do you mean som
Hi!
I had written earlier that I wanted to compare the dipole moments of a few
proteins and that the Mtot and Aver files were giving me diametrically
opposite results. The proteins with the highest dipole moments according to
Mtot were the ones with the lowest dipole moments according to aver and
Hi!
I was comparing the dipole moments of a few proteins. The results of the
Mtot and the aver files are diametrically opposite to each other. The
proteins with the max dipole moments according to the Mtot files, are the
ones with the least dipole moments according to the aver files. What is the
d
Hi!
I'm simulating a heterodimer, with the help of your lysoyme tutorial. The
simulation runs smoothly till the production MD step.
I gave these commands:
gmx_mpi grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr
time -p mpirun gmx_mpi mdrun -v -deffnm md
I kept md.mdp identica
istinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
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Hi!
I'm simulating a heterodimer. The simulation goes really smoothly till the
MD production step where I get an error saying the topol file is
inaccessible. Can you please help?
Thank you in advance and regards,
Raag
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Hi! Do you have any tutorials for MPI, please?
Regards,
Raag
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Hi!
What changes do I make to the mdp files provided by you in the lysozyme
tutorial, to make it a 500ns simulation?
Thanks in advance!
Regards,
Raag
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Hi!
I was calculating the Gibbs' free energy of the tubulin heterodimer and
gave the command:
gmx grompp -f /Applications/md/tutorial/gibbs/MDP/EM/em_steep_0.mdp -c
/Applications/md/tutorial/gibbs/1TUB_solv.gro -p
/Applications/md/tutorial/gibbs/topol.top -o min0.tpr
I got this error:
WARNING 1
Hi!
When I give the command:
perl write_sh.pl job.sh
I get this error:
readline() on closed filehandle IN at write_sh.pl line 19.
Can you please help out? Thank you in advance!
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Hi!
Thank you for your previous reply. You were right, my file was getting
modified. I had not saved the page directly but had copy-pasted it in a
textedit file.
I am again stuck, though. I was trying to run job_0.sh and when I gave the
command:
gmx grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c
$FREE
error at write_mdp.pl line 4, near "*\expandedcolortbl"
syntax error at write_mdp.pl line 4, near "cssrgb\"
syntax error at write_mdp.pl line 5, near "paperw11900\"
"use" not allowed in expression at write_mdp.pl line 12, at end of line
syntax error a
Hi!
How can I calculate Gibbs' free energy from the potential energy values
obtained from the MD simulation?
Regards,
Raag
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Hi!
I acetylated K40 my heterodimer's PDB file using PyTMs in PyMOL. Now I need
to simulate it using GROMACS. Which force field would be the best for this
purpose?
Thank you in advance!
Regards,
Raag
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? ?)
>4. Hbond residence time (Marcelo Dep?lo)
>5. addition of an isopeptide bond and its simulation (Raag Saluja)
>6. CG Graphene - dihedral problem/parameter (Sajjad Kavyani)
>7. Re: User Defined Potentials (Vytautas Rakeviius)
>
>
> ---
Hi!
I need to study the effect of post-translational modifications on the
biophysical properties of my protein. This involves the addition of an
isopeptide bond to the primary chain of the C-terminal tail.
How may I add this isopeptide bond? And then which force field can I use to
simulate it?
command I used was:
genion -s ions.tpr -o PDB_solv_ions.gro -p topol.top -pname K -nname CL -np
84300
Is there a way to add ions additional to the solvent molecules, instead of
replacing them?
Thank you and regards,
Raag Saluja
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Hi!
I wanted to see the effect of mutations on a protein. So I mutated the
protein using chimera and then calculated the potential energy and all
using Gromacs.
Is there a command, after the energy equilibration step, that I can use to
find the free energy?
--
Regards,
Raag
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Hi!
A colleague of mine is having a little problem with the gromacs mailing
list. She says she subscribed to it, but when she posts, she gets no reply.
She does get the digest, however.
She asked me to ask you if you could kindly help her.
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Regards,
Raag
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* Plea
ves the pdb as 333leu.pdb.
>
> Best,
>
>
> --
> Dr. Matej Repic
> Ecole Polytechnique F?d?rale de Lausanne
> Laboratory of Computational Chemistry and Biochemistry
> SB - ISIC ? LCBC
> BCH 4108
> CH - 1015 Lausanne
> ---
Hi!
Gromacs is a beautiful software! I have been able to understand the
dynamics of this protein I was trying to study.
I wanted to see how the various amino acids could affect its dynamics. So I
wanted to mutate the protein by replacing one particular amino acid by
another one. How may I do tha
Hi!
I tried plotting the potential energy of my molecule using xmgrace. But it
gave a warning:
Warning: locale not supported by Xlib, locale set to C
Xmgrace opened but I could see no plot.
I am new to computational biology. I am using gromacs on a mac.Can you
please guide as to how I should
> Today's Topics:
>
>1. Re: Comparing various MD packages (Mark Abraham)
>2. Re: Probable bug in 5.0.4 gmx enemat (Mark Abraham)
>3. Re: Probable bug in 5.0.4 gmx enemat (Mark Abraham)
>4. Fatal error: Residue 'GTP' not found in residue
Hi!
I was trying to simulate tubular (1TUB.pdb). I could run the pdb.gmx step.
I added the water molecules. But when I defined the force field (I chose
15), it gave an error. It said, "
Fatal error:
Residue 'GTP' not found in residue topology database"
Please guide!
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Regards,
Raag
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Gro
I was trying to download grimaces. But it says, "No such file or directory"
I tried make, but that too gave an error. It said, "No targets specified
and no make file found".
I tried installing version 5.1, 5.0 and 4.6. However, the same error
persists. Please help!
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Regards,
Raag
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