PMF calculation input files

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Mon Aug 22 2016 - 10:30:28 CDT

Hi all,

I am trying to run US-only PMF calculations with harmonic restraints
for ion permeation through a three-fold pore that is part of a
spherical protein (according to the PMF tutorial) and getting some
errors that I am trying to eliminate. I would like to make sure I
understand everything that goes into the input files correctly.

The reaction coordinate is z-axis that goes more or loss through the
middle of the channel. To create pdb files for each window I moved the
atom 2A down the channel and equilibrated the system for 300ps, then
took the last snapshot, and equilibrated again, thus creating 14
separate simulations where the ion was at a new position.

My PMF configuration and input files are in the end of this message.
The questions I have are the following:

In the configuration file:

1) Do I understand it correctly, that for coordinates I have to use
the pdb that defines the new window, and for
binCoordinates/extendedSystem I use the associated restart
equilibration files?

2) Is the first timestep supposed to be 0 for each separate window?

3) When I ran my simulations for each window there were no
constraints, do I still need the constraint section in the PMF
configuration file? I used consref ../../input/rest6.ref that is no
different from my original starting pdb file (after it was minimized
and equilibrated and before I started moving the ion through the
pore). Does it have to be a pdb for each new window, or the original
file, or no file at all?

In the colvar input file:

1) Do lowerboundary and upperboundary define window size or the length
of the ion pathway? (confused because in the manual it seems to be the
length of the pathway). So if my channel starts at 136 and ends at
108, I would have lowerboundary 134.0 upperboundary 136.0 for
window 1, lowerboundary 132.0 upperboundary 134.0 for window 2, and so
on. Is this correct?

2) Is "centers" a physical center of the window? So, if the window is
between 134 and 136 then the centers 135?

3) For ref I listed all CA atoms of the three chains that define the
pore. Does it make sense?

I'd very much appreciate comments on any of these questions. Thanks in advance!!

Olga

P.S. The input files are below:

set num 2

#############################################################
## JOB DESCRIPTION ##
#############################################################

# ABF of Fe2+ in ferritin, window 1

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure final.psf
coordinates w2.pdb

binCoordinates w2.restart.coor
extendedSystem w2.restart.xsc

set temperature 300
set outputname win${num}_out

firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters ../../toppar/par_all36_prot.prm
parameters ../../toppar/metals/CHARMM_METAL/par_all22_prot_metals.inp
temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 14.0

# Integrator Parameters
timestep 2.0 ;# 2fs/step (only if needed to finish quickly)
rigidBonds water ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

# Constant Temperature Control
langevin on ;
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens

wrapAll on

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0

# Constant Pressure Control (variable volume)
if {0} {
useGroupPressure yes ;
useFlexibleCell no ;
useConstantArea no ;

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature
}

# Output
outputName $outputname

restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100

commotion yes

#############################################################
## EXTRA PARAMETERS ##
#############################################################

constraints on
consexp 2
consref ../../input/rest6.ref
conskfile ../../input/rest6.ref
conskcol O
selectConstraints on
selectConstrX off
selectConstrY off
selectConstrZ on

colvars on
colvarsConfig US-win${num}.in

#margin 5

#############################################################
## EXECUTION SCRIPT ##
#############################################################

run 150000 ;#

Colvar input file:

colvarsTrajFrequency 20

colvar {
   name Translocation

   width 0.1

   lowerboundary 132.0
   upperboundary 134.0

   lowerwallconstant 100.0
   upperwallconstant 100.0

   distanceZ {
      main {
         atomnumbers { 291491 }
      }
      ref {
         atomnumbers {
5 19 30 47 63 87 104 118 139 156 173 185 196 211 221 231 250 264 288
305 324 338 357 372 391 412 422 433 454 470 491 510 521 538 549 570
591 611 623 647 659 671 687 697 716 738 752 772 782 804 825 845 864
881 898 909 926 941 956 980 995 1012 1022 1037 1059 1078 1095 1117
1136 1153 1167 1184 1208 1215 1222 1246 1265 1285 1304 1321 1333 1352
1369 1393 1405 1417 1428 1440 1452 1476 1491 1502 1509 1528 1542 1552
1569 1584 1595 1605 1624 1641 1660 1675 1697 1711 1727 1741 1758 1769
1788 1807 1822 1841 1858 1880 1899 1909 1923 1935 1957 1971 1985 1997
2014 2033 2044 2056 2076 2095 2110 2124 2141 2162 2181 2195 2210 2227
2243 2265 2275 2294 2316 2331 2350 2357 2369 2386 2402 2416 2430 2449
2473 2495 2512 2519 2531 2543 2558 2569 2576 2595 2605 2620 2641 2660
2680 2692 2714 2731 2745 2764 2774 2788 2799 2816 2832 2856 2873 2887
2908 2925 2942 2954 2965 2980 2990 3000 3019 3033 3057 3074 3093 3107
3126 3141 3160 3181 3191 3202 3223 3239 3260 3279 3290 3307 3318 3339
3360 3380 3392 3416 3428 3440 3456 3466 3485 3507 3521 3541 3551 3573
3594 3614 3633 3650 3667 3678 3695 3710 3725 3749 3764 3781 3791 3806
3828 3847 3864 3886 3905 3922 3936 3953 3977 3984 3991 4015 4034 4054
4073 4090 4102 4121 4138 4162 4174 4186 4197 4209 4221 4245 4260 4271
4278 4297 4311 4321 4338 4353 4364 4374 4393 4410 4429 4444 4466 4480
4496 4510 4527 4538 4557 4576 4591 4610 4627 4649 4668 4678 4692 4704
4726 4740 4754 4766 4783 4802 4813 4825 4845 4864 4879 4893 4910 4931
4950 4964 4979 4996 5012 5034 5044 5063 5085 5100 5119 5126 5138 5155
5171 5185 5199 5218 5242 5264 5281 5288 5300 5312 5327 5338 5345 5364
5374 5389 5410 5429 5449 5461 5483 5500 5514 5533 5543 5557 5568 5585
5601 5625 5642 5656 5677 5694 5711 5723 5734 5749 5759 5769 5788 5802
5826 5843 5862 5876 5895 5910 5929 5950 5960 5971 5992 6008 6029 6048
6059 6076 6087 6108 6129 6149 6161 6185 6197 6209 6225 6235 6254 6276
6290 6310 6320 6342 6363 6383 6402 6419 6436 6447 6464 6479 6494 6518
6533 6550 6560 6575 6597 6616 6633 6655 6674 6691 6705 6722 6746 6753
6760 6784 6803 6823 6842 6859 6871 6890 6907 6931 6943 6955 6966 6978
6990 7014 7029 7040 7047 7066 7080 7090 7107 7122 7133 7143 7162 7179
7198 7213 7235 7249 7265 7279 7296 7307 7326 7345 7360 7379 7396 7418
7437 7447 7461 7473 7495 7509 7523 7535 7552 7571 7582 7594 7614 7633
7648 7662 7679 7700 7719 7733 7748 7765 7781 7803 7813 7832 7854 7869
7888 7895 7907 7924 7940 7954 7968 7987 8011 8033 8050 8057 8069 8081
8096 8107 8114 8133 8143 8158 8179 8198 8218 8230 8252 8269 8283 8302
         }
      }
      axis ( 0.0, 0.0, 1.0 )
   }
}

harmonic {
        name Z
    colvars Translocation
   centers 135
        forceConstant 0.025;# 2.5 * 0.1^2 = 0.025
}

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