Dear Chris,
Thank you so much for providing the scripts and such detailed instructions. I
was trying to load the gromacs module that is already available and was unable
to get it to run.
Thanks to you, I now have a working gromacs installation.
On Thursday, October 10, 2013 2:59 PM,
On 10/11/13 1:34 AM, Mass wrote:
Dear Mark,
Thanks for your comments, I uninstalled my previous Gromacs version ( from
Ubuntu software centre I just removed it) . and followed the dirty and quick
installation on Gromacs website
tar xfz gromacs-4.6.3.tar.gz
cd gromacs-4.6.3
mkdir build
cd
Hi Justin,
Sorry for the mistake,
I typed in terminal
do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc
Secondary_Structure_analysis_original_dss.xvg -ssdump
and got the following error,
Program do_dssp, VERSION 4.6.3
Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line:
On 10/11/13 8:12 AM, Mass wrote:
Hi Justin,
Sorry for the mistake,
I typed in terminal
do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc
Secondary_Structure_analysis_original_dss.xvg -ssdump
and got the following error,
Program do_dssp, VERSION 4.6.3
Source code file:
Dear Gromacs user,
Can anyone tell me how to arrange for my login scripts to source gromacs
automatically? Justin just point that to me and in Gromacs website it is
written search the web for that, anyone know how to do that?
Thanks
On Saturday, October 12, 2013 1:12 AM, Mass
On 10/11/13 8:57 AM, Mass wrote:
Dear Gromacs user,
Can anyone tell me how to arrange for my login scripts to source gromacs
automatically? Justin just point that to me and in Gromacs website it is written
search the web for that, anyone know how to do that?
It depends on your shell. In
Maintaining your login scripts is a basic UNIX issue, not a GROMACS issue.
Google knows a lot more about it than anybody here ;-)
Mark
On Fri, Oct 11, 2013 at 2:57 PM, Mass masstransfer_2...@yahoo.com wrote:
Dear Gromacs user,
Can anyone tell me how to arrange for my login scripts to source
Hi everyone. I am a relatively new user of GROMACS having recently needed to
carry out research on proteins aggregation.
I am currently building a DMPC/DMPG 1:1 membrane by assembling individual
DMPC and DMPG lipid molecules and then using genconf to generate the amount
of lipids needed. The DMPC
Hi gromacs users,
I tried to add new bonded interactions to the ffbonded.itp file in gromos96,
but I am confused about the used parameters in the descriptions. Here is an
example:
#define gb_10.1000 1.5700e+07
; H - OA 750
The equation used in gromos is Vb(r_ij)=(1/4) k_ij
On 10/11/13 12:24 PM, superpc wrote:
Hi everyone. I am a relatively new user of GROMACS having recently needed to
carry out research on proteins aggregation.
I am currently building a DMPC/DMPG 1:1 membrane by assembling individual
DMPC and DMPG lipid molecules and then using genconf to
On 10/11/13 12:40 PM, Ehsan Sadeghi wrote:
Hi gromacs users,
I tried to add new bonded interactions to the ffbonded.itp file in gromos96,
but I am confused about the used parameters in the descriptions. Here is an
example:
#define gb_10.1000 1.5700e+07
; H - OA 750
The
On 10/11/13 1:31 PM, Ehsan Sadeghi wrote:
Thanks Justin.
Do you know how can I find these coefficients for the atom interactions which
are not defined in Gromos? I have (-(CF2CF2)4 -)(-O-CF2CF(CF3 )-O-CF2 CF2-SO3H)
molecule. I need C-F, C-S, C-S-O interactions. Can I use predefined ones?
Hi all,
I recently compared the total energy of 2 simulations:
lysozyme in water / NVE ensemble / single precision
lysozyme in water / NVE ensemble / double precision
... and what I found was quite ... disturbing (see the attached figure -
plots of the total energy). I observe a constant drift
Hi, Guillaume-
No one can tell you if you did anything wrong if you didn't tell us
what you did! There are literally thousands of combinations of
options in running an NVE simulation, a substantial fraction of which
are guaranteed not to conserve energy.
If you post the files (inputs and
On Oct 11, 2013 7:59 PM, Guillaume Chevrot guillaume.chev...@gmail.com
wrote:
Hi all,
I recently compared the total energy of 2 simulations:
lysozyme in water / NVE ensemble / single precision
lysozyme in water / NVE ensemble / double precision
... and what I found was quite ... disturbing
Hi,
sorry for my last post! I re-write my e-mail (with some additional
information) and I provide the links to my files ;-)
I compared the total energy of 2 simulations:
lysozyme in water / NVE ensemble / single precision / Gromacs 4.6.3
lysozyme in water / NVE ensemble / double precision /
Didn't see any problem in the .mdp. -4500 kJ/mol in 10ns over (guessing)
30K atoms is 0.015 kJ/mol/ns/atom. k_B T is at least 100 times larger than
that. I bet the rest of the lysozyme model physics is not accurate to less
than 1% ;-) There are some comparative numbers at
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