Hi Jun,
I think that may be as close as you will be able to get. Check the charmm
psf file and the AMBER prmtop file for the charges - specifically the
number of decimal places and note that the AMBER values are scaled by
18.2223 (it might be a 'slightly' different scaling for charges converted
from charmm so check this). I suspect there is a difference in the number
of decimal places - I remember at the time we validated things we made a
special prmtop that would take many more decimal places. So this may be
where the difference is coming from.
All the best
Ross
On 9/3/13 10:54 AM, "Jun Feng" <jufeng.mail.wvu.edu> wrote:
>Dear Dr. Ross Walker,
>Thank you for your suggestion.
>I am now able to match the VDW energy between CHARMM and AMBER. For ELEC,
>though the PME parameters are the same, there is some difference in energy
>which is consistent with the AMBER test case of DHFR.
>CHARMM:
> cton=ctof=9, no shake
> kappa 0.340 pmEwald order 4 fftx 108 ffty 108
>fftz 108
>ENER ENR: Eval# ENERgy Delta-E GRMS
>ENER INTERN: BONDs ANGLes UREY-b DIHEdrals
> IMPRopers
>ENER CROSS: CMAPs PMF1D PMF2D PRIMO
>ENER EXTERN: VDWaals ELEC HBONds ASP
>USER
>ENER IMAGES: IMNBvdw IMELec IMHBnd RXNField
> EXTElec
>ENER EWALD: EWKSum EWSElf EWEXcl EWQCor
>EWUTil
> ---------- --------- --------- --------- ---------
> ---------
>ENER> 0-185057.38479 30034.40797 14.18259
>ENER INTERN> 5091.22704 17744.99438 5862.57551 18429.68264
> 312.64340
>ENER CROSS> -45.81685 0.00000 0.00000 0.00000
>ENER EXTERN> 7877.73384-183453.70289 0.00000 0.00000
> 0.00000
>ENER IMAGES> -1103.32132 -11082.53004 0.00000 0.00000
> 0.00000
>ENER EWALD> 3211.9069-1409623.2881 1361720.5107 0.0000
>0.0000
>
>AMBER
> cut=9, no shake
> ew_coeff=0.340,nfft1=108,nfft2=108,nfft3=108,order=4,vdwmeth=0
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
> -803.1
> Etot = -185048.1581 EKtot = 0.0000 EPtot =
>-185048.1581
> BOND = 5091.2270 ANGLE = 17744.9944 DIHED =
>18431.1978
> UB = 5862.5755 IMP = 312.6434 CMAP =
>-45.8167
> 1-4 NB = 3842.7942 1-4 EEL = 28245.3711 VDWAALS =
> 2931.6172
> EELEC = -267464.7621 EHBOND = 0.0000 RESTRAINT =
>0.0000
> EKCMT = 0.0000 VIRIAL = 16101.9497 VOLUME =
> 928651.5199
> Density =
>1.0114
>
>Summary:
>VDW ELEC
>CHARMM 6774.41 -239227
>AMBER 6774.4114 -239219.391
>
>Jun Feng
>
>
>
>On Fri, Aug 30, 2013 at 6:10 PM, Ross Walker <ross.rosswalker.co.uk>
>wrote:
>
>> Hi Jun,
>>
>>
>> Charmm uses a switching function for the VDW while AMBER uses a long
>>range
>> continuum correction - which don't match obviously. Neither is more
>>wrong
>> than the other - they are both wrong. ;-)
>>
>> For sanity turn off any switching function in charmm and in amber set
>> vdwmeth=0 in the ewald namelist and you should be able to make the VDW
>> terms match. I don't recommend running with this though - better just to
>> use the default of (vdwmeth=1) when running the charmm forcefield in
>>AMBER.
>>
>> Note you should be able to get EELEC to match as well - you just have to
>> monkey with the ewald coefficient and FFT settings to make sure they are
>> exactly the same in both codes.
>>
>> Note AMBER and Charmm do shake in different ways as well so for a
>>perfect
>> comparison you should turn off shake in both runs.
>>
>> See:
>>
>> $AMBERHOME/test/chamber/md_engine/dhfr_cmap_pbc
>>
>> All the best
>> Ross
>>
>>
>> On 8/30/13 2:55 PM, "Jun Feng" <jufeng.mail.wvu.edu> wrote:
>>
>> >Dear CHAMBER developers:
>> >I tried to compare energy in AMBER and CHARMM under PBC. My workflow
>>is:
>> >1. created psf and pdb in CHARMM with c36 FF
>> >2. use CHAMBER to generate prmtop and inpcrd
>> >3. run one step energy calculation in CHARMM and pmemd under PBC using
>> >PME,
>> >compare energy. cut=9 in AMBER, cton=ctoff=9, cutoff=12 in CHARMM
>> >Result:
>> >I tried several systems and VDW energy is significantly differently
>>under
>> >PBC in all cases. But VDW energy is exactly the same in vacumm without
>> >PBC(in another thread).
>> >I provided one output of energy calculation under PBC:
>> >#CHARMM
>> >ENER ENR: Eval# ENERgy Delta-E GRMS
>> >ENER INTERN: BONDs ANGLes UREY-b DIHEdrals
>> > IMPRopers
>> >ENER CROSS: CMAPs PMF1D PMF2D PRIMO
>> >ENER EXTERN: VDWaals ELEC HBONds ASP
>> >USER
>> >ENER IMAGES: IMNBvdw IMELec IMHBnd RXNField
>> > EXTElec
>> >ENER EWALD: EWKSum EWSElf EWEXcl EWQCor
>> >EWUTil
>> > ---------- --------- --------- --------- ---------
>> > ---------
>> >ENER> 0-182266.18440 27243.20758 14.18262
>> >ENER INTERN> 5091.22704 17744.99438 5862.57551 18429.68264
>> > 312.64340
>> >ENER CROSS> -45.81685 0.00000 0.00000 0.00000
>> >ENER EXTERN> 10368.05537-183453.70289 0.00000 0.00000
>> > 0.00000
>> >ENER IMAGES> -809.55028 -11082.53004 0.00000 0.00000
>> > 0.00000
>> >ENER EWALD> 3219.0147-1409623.2881 1361720.5107 0.0000
>> >0.0000
>> >
>> >#AMBER
>> >NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
>> >-1222.4
>> > Etot = -187850.8243 EKtot = 0.0000 EPtot =
>> >-187850.8243
>> > BOND = 5091.2270 ANGLE = 17744.9944 DIHED =
>> >18431.1978
>> > UB = 5862.5755 IMP = 312.6434 CMAP =
>> >-45.8167
>> > 1-4 NB = 3842.7942 1-4 EEL = 28245.3711 VDWAALS =
>> >129.0351
>> > EELEC = -267464.8461 EHBOND = 0.0000 RESTRAINT =
>> >0.0000
>> > EKCMT = 0.0000 VIRIAL = 24509.4032 VOLUME =
>> > 928651.5199
>> > Density =
>> >1.0114
>> >
>> > CHARMM AMBER
>> >VDW total 9558.55 3971.8293
>> >ELEC total -239219 -239219.475
>> >Please also note the difference in dihedrals
>> >
>> >I understand that VDW energy is sensitive to cutoff, but can anybody
>> >explain the HUGE and significant difference in VDW energy? I am really
>> >puzzled.
>> >
>> >Jun Feng
>> >_______________________________________________
>> >AMBER mailing list
>> >AMBER.ambermd.org
>> >http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
>--
>Jun Feng
>Postdoc Fellow
>Blake Mertz Research Group
>Department of Chemistry
>West Virginia University
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Received on Tue Sep 03 2013 - 11:30:03 PDT
