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 - 20:00:03 PDT
