Thanks a lot for your suggestions.
On Mon, Dec 19, 2011 at 21:00, David Mobley wrote:
> Yes, changing the net charge of the system is something that is rather
> complicated in fact (one can plunge ahead and do it while ignoring the
> complications, but the results will typically be rather system
aiswarya pawar wrote:
I get an error like this=
Step 43230, time 86.46 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.033583, max 1.621884 (between atoms 2032 and 2030)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
I get an error like this=
Step 43230, time 86.46 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.033583, max 1.621884 (between atoms 2032 and 2030)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2032 2030 90.00.44
priya thiyagarajan wrote:
hello sir,
Thanks for your reply.
initially i tried with pdb2gmx command.but i got error.
as i said mine is a cyclicheptapeptide. my fattyacid residue type is BFC.
when i performed
pdb2gmx -f protein.pdb -p protein.top -o protein.gro -ignh
it showed error as
*Proc
hello sir,
Thanks for your reply.
initially i tried with pdb2gmx command.but i got error.
as i said mine is a cyclicheptapeptide. my fattyacid residue type is BFC.
when i performed
pdb2gmx -f protein.pdb -p protein.top -o protein.gro -ignh
it showed error as
*Processing chain 2 'A' (16 atoms,
lina wrote:
Hi,
I have very high frequency meeting below error:
[hostname-c06:07555] *** Process received signal ***
[hostname-c06:07555] Signal: Segmentation fault (11)
[hostname-c06:07555] Signal code: Address not mapped (1)
[hostname-c06:07555] Failing at address: 0x2aaab3248120
[hostname-
Hi,
I have very high frequency meeting below error:
[hostname-c06:07555] *** Process received signal ***
[hostname-c06:07555] Signal: Segmentation fault (11)
[hostname-c06:07555] Signal code: Address not mapped (1)
[hostname-c06:07555] Failing at address: 0x2aaab3248120
[hostname-c06:07555] [ 0]
What is your interpretation?
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is
Dear All
I run g_density on a membrane protein.
Here are the results
http://elisacarli.altervista.org/densityhead.jpg
http://elisacarli.altervista.org/tailsDensity.jpg
Could you help me to give an interpretation to my analysis?
Thank in advance--
gmx-users mailing listgmx-users@gromacs.
Rohit Farmer wrote:
Dear Users,
I am trying to run my simulation in parallel using above 40 threads on a
cluster using qsub system but i am getting the following errors
Fatal error:
The number of nodes you selected (43) contains a large prime factor 43.
In most cases this will lead to bad
priya thiyagarajan wrote:
hello sir,
Thanks for your reply..
i like to know is it better to do x2top for my whole protein instead of
seperating fattyacid from aminoacid to generate rtp file and top file
since mine is a cyclicheptapeptide..
so that i can use that top file for doing my energy
hello sir,
Thanks for your reply..
i like to know is it better to do x2top for my whole protein instead of
seperating fattyacid from aminoacid to generate rtp file and top file
since mine is a cyclicheptapeptide..
so that i can use that top file for doing my energy minimization ,position
restr ad
Dear Users,
I am trying to run my simulation in parallel using above 40 threads on a
cluster using qsub system but i am getting the following errors
Fatal error:
The number of nodes you selected (43) contains a large prime factor 43.
In most cases this will lead to bad performance. Choose a n
Dear jusitn Thank you for your previous reply.
I am
doing Umbrella sampling using plumed-gromacs. for that i have done umbrella
pulling using gromacs only
I have extracted the frame of reference from 120ps to 360ps . i am u
Yes, changing the net charge of the system is something that is rather
complicated in fact (one can plunge ahead and do it while ignoring the
complications, but the results will typically be rather system-size
dependent and essentially wrong). For more details refer to the Kastenholz
and Hunenberge
simon sham wrote:
Hi,
I have a question on how to calculate the metal ion position in a
protein in a simulation.
To be more more specific, I would like to make sure the metal ion stay
in the binding site throughout the simulation, and not sure which
analysis function to use.
I have tried g
Hi,
I have a question on how to calculate the metal ion position in a protein in a
simulation.
To be more more specific, I would like to make sure the metal ion stay in the
binding site throughout the simulation, and not sure which analysis function to
use.
I have tried g_rms, and did not work
priya thiyagarajan wrote:
hello sir,
thanks for your reply..
The thing is i seperated my fattyacid portion from aminoacid..
so carbon missing its bond.
That 1st carbon linked to c, one double bonded o and glu aminoacid...
how i need to model my input..
shall i need to draw my fattyacid p
hello sir,
thanks for your reply..
The thing is i seperated my fattyacid portion from aminoacid..
so carbon missing its bond.
That 1st carbon linked to c, one double bonded o and glu aminoacid...
how i need to model my input..
shall i need to draw my fattyacid portion alone in chemsketch and th
Hi
I want to run an NPT simulation with all h-bonds constrained. How does
grompp identify the Hydrogen atoms given that forcefield labels like HA,
HC, HE are used. Is it the mass?
Many Thanks
Gavin
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