Hi Ashutosh.
It is hard to tell what is going wrong without having more information regarding your system. Other experienced people might be able to chime in but here are a few thoughts:
Did you perform simulated annealing before cooling down the system? If yes, did you see a smooth transition from replica 1 to replica 36? If yes, you probably do not even need to cool down all the way to zero, by equilibrating at 300 you can get a good idea about the conformational change you want to observe.
Regarding your input file: since you are using shake it implies that hydrogen bond lengths are not important in the transition, so you can exclude those atoms from tgtfitmask and tgtrmsmask and save some time. In general, including all the atoms from residue 1 to 6227 may be overkill.
Best,
Delaram
________________________________________
From: Ashutosh Shandilya <scfbioiitd.gmail.com>
Sent: Thursday, March 14, 2019 12:04 PM
To: AMBER Mailing List
Subject: [AMBER] PNEB simulation transition
I ran PNEB simulation with 36 beads till heating the structure transitions
were smooth but while cooling for the first 12 beads (frames) there is no
change in structures(almost zero rmsd change) and from frame 13 to 36 it
seems fine. Could anyone suggest what could be the problem.
This is my input file for cooling
--------------------------------------------------
UDG NEB M
&cntrl
imin = 0, irest = 1, ntx = 5, nscm = 0,
nstlim = 1000000, dt = 0.001, ntc = 2, ntf = 2, ig = -1,
ntt = 3, gamma_ln = 1000.0, tempi = 300.0, temp0 = 0.0,
ntb = 1, iwrap=1, cut = 10.0,
tgtfitmask = ":1-6227",
tgtrmsmask = ":1-6227",
ineb = 1, skmin = 20, skmax = 20,
ntpr = 5000, ntwx = 5000, ntwr = 5000,
/
&wt type='TEMP0', istep1=0, istep2=250000,
value1=300.0, value2=100.0
/
&wt type='TEMP0', istep1=250001, istep2=500000,
value1=100.0, value2=100.0
/
&wt type='TEMP0', istep1=500001, istep2=1000000,
value1=100.0, value2=0.0
/
&wt type='TEMP0', istep1=1000001, istep2=2000000,
value1=0.0, value2=0.0
/
&wt type='END'
/
Attached is the rmsd file for cooling transition.
Many thanks,
Ashutosh
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Received on Thu Mar 14 2019 - 11:30:02 PDT
