The formula used to calculate the ELE energy are different when using implicit water model or gas phase condition. When using igb=1, you have to calculate the effective born radii, which can be avoided by using igb=0. Esurf = surften * totsasa, to know how to calculate totsasa, you can refer to J. Computat. Chem., 1999, 20, 217¨C230. Because of your special CH4 structure , the value of totsasa is zero.
At 2012-09-11 10:33:27,"ÀèÓÀÐã" <52112000016.ecnu.cn> wrote:
>hello everyone,
> thank you for seeing my question.
> now i use antechamber to get butane's prmtop and inpcrd in order to do md.
>the step is that :
>the butane.gjf file is that:
>
>%nprocshared=8
>%chk=butane.chk
>#p hf/aug-cc-pvtz
>
>Title Card Required
>
>0 1
> C -1.95504700 -0.12130200 -0.00026600
> H -2.73449200 0.63462300 -0.00043100
> H -2.10051800 -0.74605700 0.87682900
> H -2.10025500 -0.74617100 -0.87732300
> C -0.56586300 0.51426100 -0.00010000
> H -0.46364000 1.15979300 -0.87061700
> H -0.46388700 1.15987700 0.87038300
> C 0.56586300 -0.51426100 0.00011200
> H 0.46365000 -1.15978100 0.87063800
> H 0.46387700 -1.15988800 -0.87036200
> C 1.95504700 0.12130200 0.00025500
> H 2.73449100 -0.63462400 0.00040500
> H 2.10050200 0.74605900 -0.87684100
> H 2.10027100 0.74616900 0.87731100
>
>antechamber -fi gcrt -fo pdb -i butane.gjf -o butane.pdb
>antechamber -i butane.pdb -fi pdb -o butane.mol2 -fo mol2 -c bcc -s 2
>parmchk -i butane.mol2 -f mol2 -o butane.frcmod
>
>vi leap.in
>source leaprc.ff03.r1
>source leaprc.gaff
>mol =loadmol2 butane.mol2
>loadamberparams butane.frcmod
>saveamberparm mol butane.prmtop butane.inpcrd
>quit
>
>tleap -s -f leap.in to gain butane.parmtop and butane.inpcrd
>then i do md . in order to keep the structure,i do one step md and read the energy of nstep=0 . i use two methods,one is that :
>md.in
> &cntrl
> imin=0,irest=0, maxcyc=1,
> cut=999.0,
> ntpr=1,
> igb=1,gbsa=1,
> ntb=0,
> /
>and we gain the md.out :::
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
> Etot = 3.4804 EKtot = 0.0000 EPtot = 3.4804
> BOND = 0.1268 ANGLE = 0.5733 DIHED = 0.4219
> 1-4 NB = 0.7007 1-4 EEL = -0.0953 VDWAALS = -0.1623
> EELEC = 0.9086 EGB = -0.1058 RESTRAINT = 0.0000
> ESURF= 1.1125
> ------------------------------------------------------------------------------
>
>
> NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS = 0.0
> Etot = 3.4804 EKtot = 0.0000 EPtot = 3.4804
> BOND = 0.1268 ANGLE = 0.5733 DIHED = 0.4219
> 1-4 NB = 0.7007 1-4 EEL = -0.0953 VDWAALS = -0.1623
> EELEC = 0.9086 EGB = -0.1058 RESTRAINT = 0.0000
> ESURF= 1.1125
> ------------------------------------------------------------------------------
>
>
> A V E R A G E S O V E R 1 S T E P S
>
>
> NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS = 0.0
> Etot = 3.4804 EKtot = 0.0000 EPtot = 3.4804
> BOND = 0.1268 ANGLE = 0.5733 DIHED = 0.4219
> 1-4 NB = 0.7007 1-4 EEL = -0.0953 VDWAALS = -0.1623
> EELEC = 0.9086 EGB = -0.1058 RESTRAINT = 0.0000
> ESURF= 1.1125
> ------------------------------------------------------------------------------
>
>
> R M S F L U C T U A T I O N S
>
>
> NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS = 0.0
> Etot = 0.0000 EKtot = 0.0000 EPtot = 0.0000
> BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000
> EELEC = 0.0000 EGB = 0.0000 RESTRAINT = 0.0000
> ESURF= 0.0000
>|E(PBS) = 0.0000
> ------------------------------------------------------------------------------
>
>
>
>the other is that::::
>vdw6.in
> &cntrl
> imin=0,irest=0, maxcyc=1,
> cut=999.0,
> ntpr=1,
> ntb=0,
> /
>and we gain the md.out::::
> ---------------------------------------------------
>| Local SIZE OF NONBOND LIST = 27
>| TOTAL SIZE OF NONBOND LIST = 27
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
> Etot = 2.4273 EKtot = 0.0000 EPtot = 2.4273
> BOND = 0.1268 ANGLE = 0.5733 DIHED = 0.4219
> 1-4 NB = 0.7007 1-4 EEL = -0.1120 VDWAALS = -0.1623
> EELEC = 0.8790 EHBOND = 0.0000 RESTRAINT = 0.0000
> ------------------------------------------------------------------------------
>
>
> NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS = 0.0
> Etot = 2.4273 EKtot = 0.0000 EPtot = 2.4273
> BOND = 0.1268 ANGLE = 0.5733 DIHED = 0.4219
> 1-4 NB = 0.7007 1-4 EEL = -0.1120 VDWAALS = -0.1623
> EELEC = 0.8790 EHBOND = 0.0000 RESTRAINT = 0.0000
> ------------------------------------------------------------------------------
>
>
> A V E R A G E S O V E R 1 S T E P S
>
>
> NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS = 0.0
> Etot = 2.4273 EKtot = 0.0000 EPtot = 2.4273
> BOND = 0.1268 ANGLE = 0.5733 DIHED = 0.4219
> 1-4 NB = 0.7007 1-4 EEL = -0.1120 VDWAALS = -0.1623
> EELEC = 0.8790 EHBOND = 0.0000 RESTRAINT = 0.0000
> ------------------------------------------------------------------------------
>
>
> R M S F L U C T U A T I O N S
>
>
> NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS = 0.0
> Etot = 0.0000 EKtot = 0.0000 EPtot = 0.0000
> BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000
> EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000
>|E(PBS) = 0.0000
> ------------------------------------------------------------------------------
>
>
>
>we know that Eele=qi*qj/dis ,so we use the same parmtop and inpcrd file ,we should get the same EEL and EELEC energy. but we see from the two md.out,they are different. so i want to know why they are different or have i something wrong?
>at the same time , i gain the CH4 prmtop and inpcrd using the same method and run md.in
> &cntrl
> imin=0,irest=0, maxcyc=1,
> cut=999.0,
> ntpr=1,
> igb=1,gbsa=1,
> ntb=0,
> /
>then the gif file is that :
>%nprocshared=8
>%chk=ch4.chk
>#p hf/aug-cc-pvtz
>
>Title Card Required
>
>0 1
> C 0.00000000 0.00000000 0.00000000
> H 0.62558200 0.62558200 0.62558200
> H -0.62558200 -0.62558200 0.62558200
> H -0.62558200 0.62558200 -0.62558200
> H 0.62558200 -0.62558200 -0.62558200
>
>and we gain the md.out file
>| # of SOLVENT degrees of freedom (RNDFS): 0.
>| NDFMIN = 9. NUM_NOSHAKE = 0 CORRECTED RNDFP = 9.
>| TOTAL # of degrees of freedom (RNDF) = 9.
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
> Etot = 0.1264 EKtot = 0.0000 EPtot = 0.1264
> BOND = 0.0807 ANGLE = 0.0906 DIHED = 0.0000
> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000
> EELEC = 0.0000 EGB = -0.0450 RESTRAINT = 0.0000
> ESURF= 0.0000
> ------------------------------------------------------------------------------
>
>
> NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS = 0.0
> Etot = 0.1264 EKtot = 0.0000 EPtot = 0.1264
> BOND = 0.0807 ANGLE = 0.0906 DIHED = 0.0000
> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000
> EELEC = 0.0000 EGB = -0.0450 RESTRAINT = 0.0000
> ESURF= 0.0000
> ------------------------------------------------------------------------------
>
>
> A V E R A G E S O V E R 1 S T E P S
>
>
> NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS = 0.0
> Etot = 0.1264 EKtot = 0.0000 EPtot = 0.1264
> BOND = 0.0807 ANGLE = 0.0906 DIHED = 0.0000
> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000
> EELEC = 0.0000 EGB = -0.0450 RESTRAINT = 0.0000
> ESURF= 0.0000
> ------------------------------------------------------------------------------
>
>
> R M S F L U C T U A T I O N S
>
>
> NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS = 0.0
> Etot = 0.0000 EKtot = 0.0000 EPtot = 0.0000
> BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000
> EELEC = 0.0000 EGB = 0.0000 RESTRAINT = 0.0000
> ESURF= 0.0000
>|E(PBS) = 0.0000
> -------------------------------------
> when i change the igb1 to igb5 or igb7 at the same time set the matching bondi,the ESURT are also zero. so I want to know why the ESURF is zero ?
>thank you very much!
>
>
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Received on Mon Sep 10 2012 - 21:00:04 PDT
