On 12/6/12 5:46 AM, Kavyashree M wrote:
Sir,
I also have come across several papers where they have done
single simulations but in recent days most of them perform
multiple trajectories for shorter period. But I am not clear how
can multiple trajectories for shorter period of time compensate
f
On 12/6/12 5:26 AM, Erik Marklund wrote:
5 dec 2012 kl. 17.26 skrev Justin Lemkul:
On 12/5/12 11:21 AM, Kavyashree M wrote:
Sir,
Thank you for your suggestions. I decided the cutoff based on
RMSD convergence. I will calculate at different time intervals.
Running multiple simulation is de
Sir,
I also have come across several papers where they have done
single simulations but in recent days most of them perform
multiple trajectories for shorter period. But I am not clear how
can multiple trajectories for shorter period of time compensate
for single extended time simulation.
Thank y
5 dec 2012 kl. 17.26 skrev Justin Lemkul:
>
>
> On 12/5/12 11:21 AM, Kavyashree M wrote:
>> Sir,
>>
>> Thank you for your suggestions. I decided the cutoff based on
>> RMSD convergence. I will calculate at different time intervals.
>> Running multiple simulation is definitely the best suggesti
Sir,
Oh! Thanks for good suggestion. Will find a way out.
Kavya
On Wed, Dec 5, 2012 at 9:56 PM, Justin Lemkul wrote:
>
>
> On 12/5/12 11:21 AM, Kavyashree M wrote:
>
>> Sir,
>>
>> Thank you for your suggestions. I decided the cutoff based on
>> RMSD convergence. I will calculate at different t
On 12/5/12 11:21 AM, Kavyashree M wrote:
Sir,
Thank you for your suggestions. I decided the cutoff based on
RMSD convergence. I will calculate at different time intervals.
Running multiple simulation is definitely the best suggestion but
due to time and machine constraint it would be difficult
Sir,
Thank you for your suggestions. I decided the cutoff based on
RMSD convergence. I will calculate at different time intervals.
Running multiple simulation is definitely the best suggestion but
due to time and machine constraint it would be difficult. Instead
I have two mesophilic simulations.
On 12/5/12 11:13 AM, Kavyashree M wrote:
Sir,
Thank you for the reply. Total simulated time is 50ns.
first 4ns is left and only 4-50ns were considered for
rmsf calculations. T1 is 300K and T2 is 363K the protein
being simulated is from Ecoli (mesophilic).
I would suggest you compare differe
Dear users,
One more question is. Is there a way to prove
my point?
Thank you
Kavya
On Wed, Dec 5, 2012 at 9:43 PM, Kavyashree M wrote:
> Sir,
>
> Thank you for the reply. Total simulated time is 50ns.
> first 4ns is left and only 4-50ns were considered for
> rmsf calculations. T1 is 300K and
Sir,
Thank you for the reply. Total simulated time is 50ns.
first 4ns is left and only 4-50ns were considered for
rmsf calculations. T1 is 300K and T2 is 363K the protein
being simulated is from Ecoli (mesophilic).
As you have mentioned I do not have replicates of simulations
hence only one 50ns
On 12/5/12 10:56 AM, Kavyashree M wrote:
Dear users,
I have simulated a homodimer (both the chains with same number
of amino acids and in same configuration) using gromacs 453 in
OPLSAA force field at 2 different temperatures (say T1 and T2). It
was noticed that the rms fluctuation of chain A
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