Re: [AMBER] not getting correct density for N,N-dimethylformamide

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Sat, 07 Dec 2013 22:12:23 +0100

Dear Sohag Biswas,

You might be interested in testing FFs generated by R.E.D. Server Dev.
& R.E.D. Python for DMF; For instance see:
http://q4mdfft:q4mdfft2012.cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF-SohagBiswas/P8737.html

resp inputs:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF-SohagBiswas/P8737/Data-R.E.D.Server/Mol_m1/input1-sm_m1.in
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF-SohagBiswas/P8737/Data-R.E.D.Server/Mol_m1/input2-sm_m1.in

ff lib (mol3 file format):
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF-SohagBiswas/P8737/Data-R.E.D.Server/Mol_m1/Mol-sm_m1-c1.mol2

frcmod file
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF-SohagBiswas/P8737/Data-R.E.D.Server/Data-Default-Proj/frcmod.known

leaprc file
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF-SohagBiswas/P8737/Data-R.E.D.Server/Data-Default-Proj/leaprc.ff13q4mdfft

if you decide to use the opls FF you might be interested by the
RESP-O1 charge model (Henchman & Essex); so re-running the job
selecting Re_Fit="On" & CHR_TYP = "RESP-O1" in the Configuration.py
file... See
http://q4md-forcefieldtools.org/REDS-Development/popup/popkeyword.php
  & http://q4md-forcefieldtools.org/RED/resp/
      
http://q4md-forcefieldtools.org/REDS-Development/Demo2-Files/Configuration.pytxt

regards, Francois


> Hi, I am Sohag Biswas, from Indian Institute of Technology Hyderabad,
> India. I am trying to simulate 1200 DMF molecules by using OPLS-AA
> parameters. After 5000 cycle minimization and 400 ps NVT running, I ran 3ns
> NPT simulation. But I am not getting the exact density. the density value
> is showing 0.7789 which is less than experimental value (0.93). Please
> somebody help me to solve this problem. Here I have given my frcmod and
> prepi input. Thank you. Yours sincerely.
>
> remark goes here
> MASS
> o 16.00 0.000
> c 12.00 0.000
> h5 1.00 0.000
> n 14.00 0.000
> c3 12.00 0.000
> h1 1.00 0.000
>
> BOND
> o -c 648.00 1.229
> c -h5 319.40 1.100
> c -n 478.20 1.335
> n -c3 330.60 1.449
> c3-h1 335.90 1.090
>
> ANGLE
> o -c -h5 53.890 120.5
> o -c -n 75.830 122.9
> c -n -c3 63.920 121.9
> h5-c -n 52.390 116.6
> n -c3-h1 49.820 109.3
> c3-n -c3 62.130 116.2
> h1-c3-h1 39.180 109.5
>
> DIHE
> o -c -n -c3 1 2.500 180.0 2.000
> c -n -c3-h1 1 0.000 0.000 0.000
> h5-c -n -c3 1 2.500 180.0 0.000
> c3-n -c3-h1 1 0.000 0.000 2.000
>
> IMPROPER
> h5-n -c -o 1.1 180.0 2.0 Using default
> value
> c -c3-n -c3 1.1 180.0 2.0 Using default
> value
>
> NONBON
> o 1.7200 0.210
> c 1.9360 0.105
> h5 1.5556 0.015
> n 1.8027 0.170
> c3 1.8700 0.060
> h1 1.5810 0.030
>
> prepi file 0 0 2
>
> This is a remark line
> molecule.res
> MOL INT 0
> CORRECT OMIT DU BEG
> 0.0000
> 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
> 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
> 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
> 4 O1 o M 3 2 1 1.540 111.208 -180.000 -0.500000
> 5 C1 c M 4 3 2 1.243 150.981 -0.000 0.500000
> 6 H1 h5 E 5 4 3 1.115 121.537 0.000 0.000000
> 7 N1 n M 5 4 3 1.367 121.866 -180.000 -0.140000
> 8 C2 c3 3 7 5 4 1.470 121.260 0.000 -0.110000
> 9 H2 h1 E 8 7 5 1.070 109.457 59.841 0.060000
> 10 H3 h1 E 8 7 5 1.070 109.495 179.886 0.060000
> 11 H4 h1 E 8 7 5 1.070 109.404 -60.124 0.060000
> 12 C3 c3 M 7 5 4 1.470 121.879 180.000 -0.110000
> 13 H5 h1 E 12 7 5 1.070 109.456 120.341 0.060000
> 14 H6 h1 E 12 7 5 1.070 109.454 -119.665 0.060000
> 15 H7 h1 E 12 7 5 1.071 109.437 0.340 0.060000
>
>
> LOOP
>
> IMPROPER
> H1 N1 C1 O1
> C3 C2 N1 C1
>
> DONE
> STOP



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Received on Sat Dec 07 2013 - 13:30:03 PST