On 13/03/2011 8:53 AM, mohsen ramezanpour wrote:
Dear All
I run a simulation for 4 days.
Unfortunately it terminated,but not completely,1 steps from 2
has done.
Is there any way to run the continue of my files?
Thanks in advance for your guidances
Best Regards
http://www.gromacs.org
Dear gmx users,
I just started with gromacs.
Can you help me to find my mistake? I already asked about it, but I did not
understand what to do exactly in my case.
I try to run to add a new *isopeptide bone* to connect Lys and Gly (to make
a tetramer of *ubiquitin*). I use AMBER99 force field, Gr
On 13/03/2011 8:55 PM, Yulian Gavrilov wrote:
Dear gmx users,
I just started with gromacs.
Can you help me to find my mistake? I already asked about it, but I
did not understand what to do exactly in my case.
I try to run to add a new *isopeptide bone* to connect Lys and Gly (to
make a tet
Thank you!
I use the correct “O” in Gly according to .rtp and I checked it with vmd.
There is really a new isopeptide bond. When there is no bond, after
minimization and equilibration, Gly and Lys just close to each other but
they are not connected (in vmd). In my case they are connected (in vmd,
On 13/03/2011 9:53 PM, Yulian Gavrilov wrote:
Thank you!
I use the correct “O” in Gly according to .rtp and I checked it with
vmd. There is really a new isopeptide bond. When there is no bond,
after minimization and equilibration, Gly and Lys just close to each
other but they are not connect
Yes, I checked topol.top. There are all isopeptide bonds ,that I want
(according to atom contacts, angles, etc.)
2011/3/13 Mark Abraham
> On 13/03/2011 9:53 PM, Yulian Gavrilov wrote:
>
> Thank you!
>
> I use the correct “O” in Gly according to .rtp and I checked it with vmd.
> There is real
Dear all
I'd like to get the PMF using g_wham after umbrella sampling. I saw that PMF
profile dipend very strong from the windows selected in the z (reaction
coordinate) direction.
My idea is that the result of this method is much more qualitative than
quantitative. Are you in agreement with me
battis...@libero.it wrote:
Dear all
I'd like to get the PMF using g_wham after umbrella sampling. I saw that PMF
profile dipend very strong from the windows selected in the z (reaction
coordinate) direction.
My idea is that the result of this method is much more qualitative than
quantitativ
Thank you!
and, is there a problem if I'm over-sampling some regions in the case
where in the other regions I have got a good (not a under-one)
sampling?
This over-sampled region can invalidate my DeltaG value?
best,
Anna
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On 2011-03-13 15.15, anna wrote:
Thank you!
and, is there a problem if I'm over-sampling some regions in the case
where in the other regions I have got a good (not a under-one)
sampling?
This over-sampled region can invalidate my DeltaG value?
best,
Anna
Check our recent paper
Jochen S.
There is no such thing as over-sampling. There is no problem induced
by having more sampling in one region except in relation to the fact
that you now have less sampling in some other region. That is to say,
if you have a totally converged PMF and then sample the first half of
the umbrellas
On 13/03/2011 10:05 PM, Yulian Gavrilov wrote:
Yes, I checked topol.top. There are all isopeptide bonds ,that I want
(according to atom contacts, angles, etc.)
Perhaps I've been labouring under a misapprehension. You've mentioned an
isopeptide bond, which usually happens between a side-chain
Hi ,I compiled gromacs without any error (or so I think) over Mandrake 9.0.
When I run the demo added to gromacs I got the error message:
Fatal error: ci = -1 should be in 0 .. 1[FILE nsgrid.c, LINE 210]
from the mdrun program, does someone knows how to overcome it?
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