On Fri, Jun 5, 2015 at 2:12 PM, Mrinda Jones <mrindajones.gmail.com> wrote:
> Hi Hector,
>
> I did the simulation again using the forcefield ff14SB as suggested and
> using the scripts sent by you.
>
I wouldn't have expected this to make any difference, and the comment
about putting garlic on the computer leads me to the conclusion that his
response was sarcastic, unfortunately.
leap.log looks like this:
>
> Adding box at: x=7 y=7 z=4
> Center of solvent box is: -65.710222, -65.710222, -9.387175
> Adding box at: x=7 y=7 z=5
> Center of solvent box is: -65.710222, -65.710222, -28.161524
> Adding box at: x=7 y=7 z=6
> Center of solvent box is: -65.710222, -65.710222, -46.935873
> Adding box at: x=7 y=7 z=7
> Center of solvent box is: -65.710222, -65.710222, -65.710222
> (using default radius 1.500000 for Cl-)
> (using default radius 1.500000 for Cl-)
> (using default radius 1.500000 for Cl-)
> (using default radius 1.500000 for Cl-)
> (using default radius 1.500000 for Cl-)
> (using default radius 1.500000 for Cl-)
> Volume: 1176727.919 A^3 (oct)
> Mass > 652639.550 amu, Density > 0.921 g/cc
> (type - hence mass - of one or more atoms could not be found)
> Added 34845 residues.
> >loadamberparams frcmod.ionsjc_tip3p
> Loading parameters: /opt/apps/amber14/dat/leap/parm/frcmod.ionsjc_tip3p
> Reading force field modification type file (frcmod)
> Reading title:
> Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham
> JPCB (2008)
> > saveamberparm k file.top file.crd
> Checking Unit.
> WARNING: The unperturbed charge of the unit: 0.998000 is not zero.
>
> -- ignoring the warning.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> 1-4: angle 3452 3459 duplicates bond ('triangular' bond) or angle ('square'
> bond)
>
> 1-4: angle 3446 3454 duplicates bond ('triangular' bond) or angle ('square'
> bond)
>
> 1-4: angle 3438 3439 duplicates bond ('triangular' bond) or angle ('square'
> bond)
>
> 1-4: angle 3437 3440 duplicates bond ('triangular' bond) or angle ('square'
> bond)
>
This is strange. Do you know that you have a 3- or 4-membered ring
somewhere in your system? If not, you should check into this.
> And the summary.DENSITY looks like:
>
> 55.000 0.9855
> 60.000 0.9917
> 65.000 0.9928
> 70.000 0.9928
> 75.000 0.9935
> 80.000 0.9933
> 85.000 0.9944
> 90.000 0.9939
> 95.000 0.9937
> 100.000 0.9926
> 105.000 0.9934
> 110.000 0.9950
> 115.000 0.9927
> 120.000 0.9936
>
This is quite normal, and no indication of a problem.
>
> The out file has been run for till now...
>
> NSTEP = 5000000 TIME(PS) = 30050.000 TEMP(K) = 299.99 PRESS =
> 4.2
> Etot = -206659.9413 EKtot = 49032.6650 EPtot =
> -255692.6063
> BOND = 697.6952 ANGLE = 1842.6901 DIHED =
> 2385.6542
> 1-4 NB = 784.6829 1-4 EEL = 4981.9735 VDWAALS =
> 34935.9089
> EELEC = -301321.2111 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 23307.9527 VIRIAL = 23234.0444 VOLUME =
> 820161.0029
> Density =
> 0.9979
>
>
> RMS calculation script
>
> trajin npt_MS.mdcrd
> trajin npt_MS2.mdcrd
> trajin npt_MS3.mdcrd
> autoimage
> trajout npt_MS_all3reimg.mdcrd
> rms first out rms.out @CA,C,N, time 10.0
>
>
> The rmsd for the same shows stablising around 11 Angstrom
>
> 59610.000 10.9905
> 59620.000 11.1655
> 59630.000 11.1025
> 59640.000 11.0785
> 59650.000 11.1712
> 59660.000 11.2284
> 59670.000 11.3872
> 59680.000 11.4965
> 59690.000 11.5443
> 59700.000 11.3725
> 59710.000 11.3509
> 59720.000 11.2027
> 59730.000 11.2712
> 59740.000 11.2898
> 59750.000 11.2370
> 59760.000 11.1258
> 59770.000 11.1687
> 59780.000 11.1122
> 59790.000 11.0479
> 59800.000 11.2534
> 59810.000 11.1920
> 59820.000 11.2822
> 59830.000 11.2291
> 59840.000 11.1727
> 59850.000 11.1325
> 59860.000 11.2933
> 59870.000 11.2510
> 59880.000 11.2540
> 59890.000 11.3308
> 59900.000 11.3084
> 59910.000 11.2239
> 59920.000 11.3312
> 59930.000 11.3771
> 59940.000 11.3447
> 59950.000 11.4072
> 59960.000 11.3195
> 59970.000 11.3988
> 59980.000 11.4998
> 59990.000 11.4432
> 60000.000 11.4997
>
> What can we infer now from the results?
>
Your starting conformation is changing a *lot*. This is where you should
load your system into a molecular visualization program and try to see
what's happening. RMSD is just a single number -- it's hard to get a clear
picture of what is happening to a system with tens or hundreds of thousands
of atoms based on a single number.
> Also the density still remains less than 1 gm/cc any suggestions why?
>
I covered this in detail in my last response. As I stated in my last
response, the same kinds of artifacts and effects arise for different
reasons in different simulations. One of the most challenging tasks in our
field is to be able to identify when there is a problem in the model and
what caused that problem. Is it some silly mistake you made setting up the
system? Is it a set of bad parameters? Is it a bad starting structure
with insufficient minimization? Is the force field deficient in some way?
You need to ask yourself these kinds of questions and then look at the
output files from your simulation for clues that would support one of your
hypotheses.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jun 05 2015 - 12:00:02 PDT
