On 9/5/13 12:53 AM, Dallas Warren wrote:
Going through the GROMOS53a6 parameters, found that there appears to be an
inconsistency between what is present within the ffnonbonded.itp file and that
quoted within the paper (Ooostenbrink et al 2004
http://dx.doi.org/10.1002/Jcc.20090) for the c12
On 9/5/13 1:10 AM, Piduru Viswanath wrote:
Hi,
I have run my MD till 13 ns extending it by 500 ps simulations. But while
shifting the data from a system, accidentally I lost my tpr files. My
backup contains trr files till 13 ns (i.e. all trr files) and tpr files
till 6.5ns. How could I regener
Hello Nilesh,
it sounds like you have a similar problem to mine, except my original run
has large energy fluctuations and the rerun does not. By chance is your
gromacs version installed with mpi on? i think i have narrowed my problem to
a bug in the installation with mpi.
If you search for my "i
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To wrap this up for anyone who stumbles across this in the future:
The 'solution' I ended up going with was to avoid using hydrogen atoms in
the restraints, instead restraining to the e.g. methyl carbon and adding a
fudge factor to the restraint length to account for the C-H distance.
This results
Hi all,
Need your help to explain more about this multiple chain.I would like
to do a simulation with a multiple type identical protein. By using
the instruction that gromacs wrote in
'http://www.gromacs.org/Documentation/How-tos/Multiple_Chains', seem
that i'm a bit lost when it tells us to us th
On 9/5/13 10:09 PM, Nur Syafiqah Abdul Ghani wrote:
Hi all,
Need your help to explain more about this multiple chain.I would like
to do a simulation with a multiple type identical protein. By using
the instruction that gromacs wrote in
'http://www.gromacs.org/Documentation/How-tos/Multiple_Cha
Thanks Justin for the quick reply.
by the way after i solvated the protein with water and i change the
amount of the protein that i want for example 8 and the amount of
water that already in is 20453.But after i proceed with grompp the
result shows that my .top file have different number of config
On 9/5/13 10:31 PM, shika wrote:
Thanks Justin for the quick reply.
by the way after i solvated the protein with water and i change the
amount of the protein that i want for example 8 and the amount of
water that already in is 20453.But after i proceed with grompp the
result shows that my .top
Hi guys
do you have an idea what is causing the segmentation fault with g_cluster?
I do the following
1 . I combine trr files from different simulations using trjcat and select
backbone atoms only
trjcat -f ../../*C/runs/*/*trr -cat -n index.ndx -o trajout_combined.xtc
2. I make a new .tp
Hi guys
do you have an idea what is causing the segmentation fault with g_cluster?
I do the following
1 . I combine trr files from different simulations using trjcat and select
backbone atoms only
trjcat -f ../../*C/runs/*/*trr -cat -n index.ndx -o trajout_combined.xtc
2. I make a new .tp
Hi guys
do you have an idea what is causing the segmentation fault with g_cluster?
I do the following
1 . I combine trr files from different simulations using trjcat and select
backbone atoms only
trjcat -f ../../*C/runs/*/*trr -cat -n index.ndx -o trajout_combined.xtc
2. I make a new .tp
Hi guys
do you have an idea what is causing the segmentation fault with g_cluster?
I do the following
1 . I combine trr files from different simulations using trjcat and select
backbone atoms only
trjcat -f ../../*C/runs/*/*trr -cat -n index.ndx -o trajout_combined.xtc
2. I make a new .tp
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