Dear Amber users and developers,
I am performing Umbrella Sampling simulations to study the permeation of a small polymer fragment inside a POPC/CHL 2:1 lipid bilayer.
I built the lipid bilayer with the CHARMM GUI website and I have obtained an equilibrated structure, that I checked with the area per lipid and bilayer thickness as a function of simulation time.
I have subsequently put the polymer fragment in the simulation box and I have rebuilt the simulation box with the AddToBox utility, adding water and ions only along z.
I ran additional simulations to obtain an equilibrated system configuration and I started US simulations.
I use the following input file:
Equil
&cntrl
imin = 0,
irest = 1,
ntx = 7,
ntb = 2,
pres0 = 1.0,
ntp = 3,
taup = 2.0,
cut = 10.0,
ntc = 2,
ntf = 2,
temp0 = 310.0,
tempi = 310.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 20000000,
dt = 0.002,
ntpr = 10000,
ntwx = 10000,
ntwr = 10000,
nmropt = 1,
csurften = 3,
gamma_ten = 0.0,
ninterface = 2,
tol = 0.0000001
/
&wt type = 'DUMPFREQ', istep1 = 100 /
&wt type = 'END', /
DISANG = ref_COM.rst
DUMPAVE = Pull_dist.dat
LISTIN = POUT
LISTOUT = POUT
/
/
&ewald
skinnb = 3.0,
/
This is the ref_COM.rst file:
&rst
iat=-1,-1,
r1=-99.0,
r2=0.0,
r3=0.0,
r4=99.0,
rk2=2.5,
rk3=2.5,
iresid=0,
fxyz=0,0,1,
outxyz=1,
igr1=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,
igr2=130,264,398,606,888,1022,1156,1364,1498,1632,1766,1900,2034,2168,2376,2510,2866,3000,3208,3342,3476,3610,3744,3878,4086,4294,4576,4710,4844,4978,5112,5320,5602,5736,6018,6226,6360,6568,6850,6984,7192,7326,7534,7668,7802,7936,8144,82
78,8412,8546,8754,8888,9022,9230,9512,9646,9780,9914,10048,10182,10316,10524,10954,11088,11222,11356,11490,11624,11758,11966,12248,12382,12516,12650,12858,12992,13126,13260,13468,13676,13884,14018,14226,14434,14568,14702,14836,14970,1510
4,15238,15520,15654,15862,15996,16204,16338,16472,16606,16740,17022,17156,17438,17572,17780,17914,18270,18552,18686,18820,18954,19088,19296,19430,19786,19920,20054,20188,20322,20456,20590,20724,20858,20992,21200,
/
where atoms 1-63 belong to my polymer fragment, while atoms of igr2 are the N31 atoms of the polar heads (I essentially follow the approach explained by Dr. Dickson Callum in his tutorial). I checked the numbers and they are correct.
For some unknown reasons, I obtained this:
NSTEP = 10000 TIME(PS) = 10540.000 TEMP(K) = 309.33 PRESS = -116.3
Etot = ************** EKtot = 34089.0039 EPtot = **************
BOND = 2925.3688 ANGLE = 12094.6034 DIHED = 7501.6413
1-4 NB = 2919.0577 1-4 EEL = -42192.4792 VDWAALS = 5238.4991
EELEC = -110714.2666 EHBOND = 0.0000 RESTRAINT = **************
EAMBER (non-restraint) = -122227.5755
EKCMT = 9433.8540 VIRIAL = 10678.6782 VOLUME = 495566.9126
SURFTEN = -52.4235
Density = 1.0067
------------------------------------------------------------------------------
NMR restraints: Bond =********* Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 20000 TIME(PS) = 10560.000 TEMP(K) = 311.67 PRESS = 187.4
Etot = ************** EKtot = 34346.3750 EPtot = **************
BOND = 2985.2622 ANGLE = 12157.1242 DIHED = 7567.3432
1-4 NB = 2901.6475 1-4 EEL = -42177.9928 VDWAALS = 5504.9903
EELEC = -110692.8191 EHBOND = 0.0000 RESTRAINT = **************
EAMBER (non-restraint) = -121754.4445
EKCMT = 9541.5155 VIRIAL = 7537.2160 VOLUME = 495324.5851
SURFTEN = 86.8556
Density = 1.0072
------------------------------------------------------------------------------
NMR restraints: Bond =********* Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 30000 TIME(PS) = 10580.000 TEMP(K) = 307.85 PRESS = -10.4
Etot = ************** EKtot = 33925.5469 EPtot = **************
BOND = 3003.1912 ANGLE = 12038.2158 DIHED = 7478.7713
1-4 NB = 2874.2811 1-4 EEL = -42133.3378 VDWAALS = 5436.8241
EELEC = -110538.2867 EHBOND = 0.0000 RESTRAINT = **************
EAMBER (non-restraint) = -121840.3409
EKCMT = 9409.4898 VIRIAL = 9520.6799 VOLUME = 495200.1274
SURFTEN = -193.4285
Density = 1.0075
------------------------------------------------------------------------------
NMR restraints: Bond =********* Angle = 0.000 Torsion = 0.000
If I do not add a restraint, the system behaves nicely.
What puzzles me is that I used the same protocol and approach for the same polymer fragment in a pure DOPC membrane and I had no problems, and the obtained results are consistent.
Can you provide some suggestions?
I thank you in advance for your support!
Tommaso
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Received on Thu Jan 16 2020 - 02:00:02 PST
