On 7/17/13 10:43 AM, Sainitin Donakonda wrote:
Ok..thanks...so i will use -rerun option in final production ..step..as
follows...actually i ran 20 ns MD simulation so i used extend option to run
everything in cluster in correct time
#first 10 ns
grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
MD_10.tpr
mdrun -s MD_10.tpr *-rerun MD_20* -deffnm MD_10
#extension for 10 more ns
tpbconv -s MD_first10.tpr -extend 10000 -o md_extended_2.tpr
mdrun -s md_extended_2.tpr -deffnm MD_second10 *-rerun MD_second10* -cpi
MD_first10.cpt -np 32
Can you please tell is this commands are appropriate for production run
using -rerun option...in help manual it is mentioned that "Neighbor
You will need a new .tpr file that does not use PME. Then, I would suggest
concatenating the existing .xtc files to streamline the process. I also do not
recall whether the -rerun option works in parallel, but in any case it is
reasonably fast even in serial. Thus:
mdrun -s newtpr.tpr -rerun full20ns.xtc
searching will be performed for every frame, unless nstlist is zero"..
should i set nslist to zero in MDP file?
No. You want the neighbor list to be updated at every frame in the .xtc,
otherwise you will miss interactions and the output will likely be flawed.
-Justin
Thanks
On Wed, Jul 17, 2013 at 4:21 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 7/17/13 10:12 AM, Sainitin Donakonda wrote:
Usually i collect data after final production run...after this i take .xtc
file and analyze it using various gromacs tools ..
And there you have it. LIE is just an analysis method like anything else.
There is no purpose in my mind in reanalyzing nonbonded energies during
equilibration.
-Justin
thanks,
nitin
On Wed, Jul 17, 2013 at 3:51 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 7/17/13 9:21 AM, Sainitin Donakonda wrote:
Hi justin,
Thanks for explaination .. i already ran MD for both ligand alone and
protein ligand complex..
So now can you please tell me where should use mdrun -rerun option ..i
mean
at which stage ..should i used in Energy miniminimzation or NVT and NPT
equilibration or Production run ..
Or should i use mdrun -rerun option at every stage ...? or it should be
used only at final production run?
Which simulation stage do you normally use to collect data?
-Justin
Thanks,
Nitin
On Wed, Jul 17, 2013 at 2:59 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 7/17/13 8:54 AM, Sainitin Donakonda wrote:
Hi ,
I want to use g_lie for my protein-drug complex to get binding energy
..i
read some information that we need take care some issues if we used
PME
electrostatics..
Indeed i have used PME in my simulation..
Can any body explain which parameters to be taken care while running
g_LIE
and what is the isssue with PME ..
The long-range mesh terms are not decomposable in a pairwise manner.
LIE
assumes that all of your interactions can be broken down from additive
terms, and this is not the case with PME.
and why we should use -rerun option beofre running LIE
If you evaluate the energies from a PME simulation, the result will
be
off. If you use plain cutoffs for the dynamics, the simulation will
probably be junk. So one solution is to run the simulation with PME to
get
reasonable dynamics, then post-process via mdrun -rerun while
evaluating
energies with plain cutoffs (which one would usually increase beyond
normal
values, IIRC, but I do not use LIE myself).
-Justin
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