Dear all,
I have just installed gromacs 4.6.5 in Cygwin build on Windows 7
platform. I want to test the installation but it keeps giving the
error
./gmxtest.pl all
ERROR: Can not find executable gmx pdb2gmx in your path.
Please source GMXRC and try again.
My Gromacs is installed in the C: drive
Dear All,
I recentlly installed gromacs 5.0.1 and a few months later 5.0.4 (hoping there was adifference) as I am using terra grid with a 5.0.1 install.
Now, I noticed 2 things, trjconv_d no matter what I do can not read or convert the .trr file, even with simple -f in.trr -o out.trr or
Hi Ming
Use *-pbc mol* while using trjconv. Anyway it is not another box.
Best Regards
--
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB, INDIA
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On 4/5/15 1:10 AM, mah maz wrote:
Dear all,
I performed 2 runs one after the other. Then, I performed those 2 runs
simultaneously(no special commands were applied, I just used different
terminals with mdrun -v command) but in different directories. Results
(like msd and energies) were expected
Dear all,
I did a simulation using periodic boundary conditions pbc=xyz. It turns out
that the box is defined too small, and some atoms go to another box.
Does this affect the simulation result? If not, how to display the real model
(without separation) in VMD?
Thanks in advance,
Ming
--
Hi Ming,
You have another box in your (infinite) periodic system?
Cheers,
Tsjerk
On Sun, Apr 5, 2015 at 10:32 AM, Ming Tang m21.t...@qut.edu.au wrote:
Dear all,
I did a simulation using periodic boundary conditions pbc=xyz. It turns
out that the box is defined too small, and some atoms
Hi Tsjerk,
I defined only one box. I mean several atoms in one chain run out of the
boundary, and I can see them in the box but not in the chain. So I think maybe
they run to the nearby box because of the periodic boundary conditions.
Thanks,
Ming
-Original Message-
From:
Dear gromacs users,
I am trying to simulate liquid SO2 (Sulphur dioxide). So I tried to create
an equilibrated structure of SO2 molecules using the gmx insert-molecules
function. As I try to minimize the energy of the system, I always get this-
Em 05/04/2015 14:44, Jashimuddin Ashraf jashimuddin.ashra...@gmail.com
escreveu:
Dear gromacs users,
I am trying to simulate liquid SO2 (Sulphur dioxide). So I tried to create
an equilibrated structure of SO2 molecules using the gmx insert-molecules
function. As I try to minimize the energy
