When I have performed umbrella sampling using center of mass in cpu using following script :
#Harmonic restraints for 4.5 ang
> &rst iat=-1,-1,0
> r1=0.000000, r2=4.500000, r3=4.500000, r4=99.000000, rk2=10.000000, rk3=10.000000,
> IGR1(1)=64,IGR1(2)=65,IGR1(3)=66,IGR1(4)=67,IGR1(5)=68,IGR1(6)=69,IGR1(7)=70,IGR1(8)=71,IGR1(9)=72,IGR1(10)=73,IGR1(11)=74,IGR1(12)=75,IGR1(13)=76,IGR1(14)=77,IGR1(15)=78,IGR1(16)=79,IGR1(17)=80,IGR1(18)=81,IGR1(19)=82,IGR1(20)=83,IGR1(21)=84,IGR1(22)=85,IGR1(23)=86,IGR1(24)=87,IGR1(25)=88,IGR1(26)=89,IGR1(27)=90,IGR1(28)=91,IGR1(29)=92,IGR1(30)=93,IGR1(31)=94,IGR1(32)=95,IGR1(33)=96,IGR1(34)=97,IGR1(35)=98,IGR1(36)=99,IGR1(37)=100,IGR1(38)=101,IGR1(39)=102,IGR1(40)=103,
> IGR2(1)=198,IGR2(2)=199,IGR2(3)=200,IGR2(4)=201,IGR2(5)=202,IGR2(6)=203,IGR2(7)=204,IGR2(8)=205,IGR2(9)=206,IGR2(10)=207,IGR2(11)=208,IGR2(12)=209,IGR2(13)=210,IGR2(14)=211,IGR2(15)=212,IGR2(16)=213,IGR2(17)=214,IGR2(18)=215,IGR2(19)=216,IGR2(20)=217,IGR2(21)=218,IGR2(22)=219,IGR2(23)=220,IGR2(24)=221,IGR2(25)=222,IGR2(26)=223,IGR2(27)=224,IGR2(28)=225,IGR2(29)=226,IGR2(30)=227,IGR2(31)=228,IGR2(32)=229,IGR2(33)=230,IGR2(34)=231,IGR2(35)=232,IGR2(36)=233,IGR2(37)=234,IGR2(38)=235,IGR2(39)=236,IGR2(40)=237,
> &end
It works fine.But its not working in gpu.
If I have used this input :#Harmonic restraints for 4.5 ang
> &rst iat=1,1,0
> r1=0.000000, r2=4.500000, r3=4.500000, r4=99.000000, rk2=10.000000, rk3=10.000000,
> IGR1(1)=64,IGR1(2)=65,IGR1(3)=66,IGR1(4)=67,IGR1(5)=68,IGR1(6)=69,IGR1(7)=70,IGR1(8)=71,IGR1(9)=72,IGR1(10)=73,IGR1(11)=74,IGR1(12)=75,IGR1(13)=76,IGR1(14)=77,IGR1(15)=78,IGR1(16)=79,IGR1(17)=80,IGR1(18)=81,IGR1(19)=82,IGR1(20)=83,IGR1(21)=84,IGR1(22)=85,IGR1(23)=86,IGR1(24)=87,IGR1(25)=88,IGR1(26)=89,IGR1(27)=90,IGR1(28)=91,IGR1(29)=92,IGR1(30)=93,IGR1(31)=94,IGR1(32)=95,IGR1(33)=96,IGR1(34)=97,IGR1(35)=98,IGR1(36)=99,IGR1(37)=100,IGR1(38)=101,IGR1(39)=102,IGR1(40)=103,
> IGR2(1)=198,IGR2(2)=199,IGR2(3)=200,IGR2(4)=201,IGR2(5)=202,IGR2(6)=203,IGR2(7)=204,IGR2(8)=205,IGR2(9)=206,IGR2(10)=207,IGR2(11)=208,IGR2(12)=209,IGR2(13)=210,IGR2(14)=211,IGR2(15)=212,IGR2(16)=213,IGR2(17)=214,IGR2(18)=215,IGR2(19)=216,IGR2(20)=217,IGR2(21)=218,IGR2(22)=219,IGR2(23)=220,IGR2(24)=221,IGR2(25)=222,IGR2(26)=223,IGR2(27)=224,IGR2(28)=225,IGR2(29)=226,IGR2(30)=227,IGR2(31)=228,IGR2(32)=229,IGR2(33)=230,IGR2(34)=231,IGR2(35)=232,IGR2(36)=233,IGR2(37)=234,IGR2(38)=235,IGR2(39)=236,IGR2(40)=237,
> &endIt works fine in gpu but not working in cpu.
> &rst iat=1,1,0 works fine in gpu bt not working in cpu
> &rst iat=-1,-1,0 works fine in cpu bt not working in gpu
Thanks and Regards,
Saikat Pal
On Friday, 14 September, 2018, 10:17:25 PM IST, Bill Ross <ross.cgl.ucsf.edu> wrote:
You could output coords and energies for each step, and study right
before the first NaN closely for clues. And include the whole mdin file
w/ next question.
Bill
On 9/14/18 7:26 AM, Saikat Pal wrote:
> Dear all,I am performing umbrella sampling.But after successful minimisation, in equlibration out file I have got the following stuff:
> NMR restraints: Bond =********* Angle = 0.000 Torsion = 0.000
> ===============================================================================
>
> NSTEP = 2500000 TIME(PS) = 5000.000 TEMP(K) = NaN PRESS = NaN
> Etot = NaN EKtot = NaN EPtot = NaN
> BOND = 0.0000 ANGLE = 32013.4755 DIHED = 0.0000
> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = NaN
> EELEC = NaN EHBOND = 0.0000 RESTRAINT = **************
> EAMBER (non-restraint) = NaN
> EKCMT = 0.0000 VIRIAL = NaN VOLUME = NaN
> Density = NaN
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond =********* Angle = 0.000 Torsion = 0.000
> ===============================================================================
>
> A V E R A G E S O V E R 500 S T E P S
>
>
> NSTEP = 2500000 TIME(PS) = 5000.000 TEMP(K) = NaN PRESS = NaN
> Etot = NaN EKtot = NaN EPtot = NaN
> BOND = 0.0000 ANGLE = 32013.4755 DIHED = 0.0000
> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = NaN
> EELEC = NaN EHBOND = 0.0000 RESTRAINT = **************
> EAMBER (non-restraint) = NaN
> EKCMT = 0.0000 VIRIAL = NaN VOLUME = NaN
> Density = NaN
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond =********* Angle = 0.000 Torsion = 0.000
> ===============================================================================
>
> R M S F L U C T U A T I O N S
>
>
> NSTEP = 2500000 TIME(PS) = 5000.000 TEMP(K) = NaN PRESS = NaN
> Etot = NaN EKtot = NaN EPtot = NaN
> BOND = 0.0000 ANGLE = 0.0029 DIHED = 0.0000
> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = NaN
> EELEC = NaN EHBOND = 0.0000 RESTRAINT = 0.0000
>
> Here is my disang file:
> #Harmonic restraints for 4.5 ang
> &rst iat=-1,-1,0
> r1=0.000000, r2=4.500000, r3=4.500000, r4=99.000000, rk2=10.000000, rk3=10.000000,
> IGR1(1)=64,IGR1(2)=65,IGR1(3)=66,IGR1(4)=67,IGR1(5)=68,IGR1(6)=69,IGR1(7)=70,IGR1(8)=71,IGR1(9)=72,IGR1(10)=73,IGR1(11)=74,IGR1(12)=75,IGR1(13)=76,IGR1(14)=77,IGR1(15)=78,IGR1(16)=79,IGR1(17)=80,IGR1(18)=81,IGR1(19)=82,IGR1(20)=83,IGR1(21)=84,IGR1(22)=85,IGR1(23)=86,IGR1(24)=87,IGR1(25)=88,IGR1(26)=89,IGR1(27)=90,IGR1(28)=91,IGR1(29)=92,IGR1(30)=93,IGR1(31)=94,IGR1(32)=95,IGR1(33)=96,IGR1(34)=97,IGR1(35)=98,IGR1(36)=99,IGR1(37)=100,IGR1(38)=101,IGR1(39)=102,IGR1(40)=103,
> IGR2(1)=198,IGR2(2)=199,IGR2(3)=200,IGR2(4)=201,IGR2(5)=202,IGR2(6)=203,IGR2(7)=204,IGR2(8)=205,IGR2(9)=206,IGR2(10)=207,IGR2(11)=208,IGR2(12)=209,IGR2(13)=210,IGR2(14)=211,IGR2(15)=212,IGR2(16)=213,IGR2(17)=214,IGR2(18)=215,IGR2(19)=216,IGR2(20)=217,IGR2(21)=218,IGR2(22)=219,IGR2(23)=220,IGR2(24)=221,IGR2(25)=222,IGR2(26)=223,IGR2(27)=224,IGR2(28)=225,IGR2(29)=226,IGR2(30)=227,IGR2(31)=228,IGR2(32)=229,IGR2(33)=230,IGR2(34)=231,IGR2(35)=232,IGR2(36)=233,IGR2(37)=234,IGR2(38)=235,IGR2(39)=236,IGR2(40)=237,
> &end
> Please help me out.
>
>
>
>
>
> Thanks and Regards,
> Saikat Pal
>
>
>
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Received on Mon Sep 17 2018 - 09:00:02 PDT
