Hi, Daniel,
Thanks for the precious guidance. This what I want and the script was perfect. But I after 4000 steps the production run got this error: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered. And there is not restrain in the output as below:
wrapping first mol.: 30.51583 43.15591 74.74821
wrapping first mol.: 30.51583 43.15591 74.74821
NSTEP = 4000 TIME(PS) = 608.000 TEMP(K) = 308.07 PRESS = -237.6
Etot = -153810.1794 EKtot = 36112.7344 EPtot = -189922.9138
BOND = 578.5793 ANGLE = 1445.0337 DIHED = 2202.2790
1-4 NB = 687.3814 1-4 EEL = 7970.8282 VDWAALS = 24116.2997
EELEC = -226923.3149 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 17106.3674 VIRIAL = 20136.3763 VOLUME = 590645.1967
Density = 0.9997
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
Is there anything wrong with my restraint and control files? I tried to use small time steps but got the same error. Many thanks.
&rst iat=-1,-1,0
r1=1.300000, r2=1.800000, r3=10.000000, r4=10.500000, rk2=20.000000, rk3=0.000000,
IGR1(1)=2794,IGR1(2)=2795,IGR1(3)=2796,...
IGR2(1)=2829,IGR2(2)=2830,IGR2(3)=2831,...
nstep1=0, nstep2=0,
&end
equil NPT 10ns
equilibrate
&cntrl
imin=0,irest=1,ntx=5,nmropt=1,
nstlim=2000000000,dt=0.002,
ntc=2,ntf=2,ig=-1,
cut=10.0, ntb=2, ntp=1,pres0=1, taup=1.0,
ntpr=1000, ntwx=1000,ntwr=1000,iwrap=1,
ntt=3, gamma_ln=2.0,
temp0=310.0
/
&wt type='END' /
DISANG=DISANG.f
LISTOUT=POUT
-----Original Message-----
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Friday, 5 March 2021 2:18 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] makeDIST_RST
Hi,
This might not be exactly what you want, but cpptraj can generate sander distance restraint syntax using Amber mask syntax via the 'rst'
command, e.g. to create a distance restraint between the atoms of residues 1 and 12 in tz2.parm7:
parm test/tz2.parm7
rst :1 :12 r1 2 r2 3 r3 4 r4 5 rk2 5 rk3 5 out temp.rst
Contents of temp.rst:
&rst iat=-1,-1,0
r1=2.000000, r2=3.000000, r3=4.000000, r4=5.000000, rk2=5.000000, rk3=5.000000,
IGR1(1)=1,IGR1(2)=2,IGR1(3)=3,IGR1(4)=4,IGR1(5)=5,IGR1(6)=6,IGR1(7)=7,IGR1(8)=8,IGR1(9)=9,IGR1(10)=10,IGR1(11)=11,IGR1(12)=12,IGR1(13)=13,
IGR2(1)=196,IGR2(2)=197,IGR2(3)=198,IGR2(4)=199,IGR2(5)=200,IGR2(6)=201,IGR2(7)=202,IGR2(8)=203,IGR2(9)=204,IGR2(10)=205,IGR2(11)=206,IGR2(12)=207,IGR2(13)=208,IGR2(14)=209,IGR2(15)=210,IGR2(16)=211,IGR2(17)=212,IGR2(18)=213,IGR2(19)=214,IGR2(20)=215,IGR2(21)=216,IGR2(22)=217,
nstep1=0, nstep2=0,
&end
Hope this is helpful,
-Dan
On Thu, Mar 4, 2021 at 12:04 AM Ming Tang <m21.tang.qut.edu.au> wrote:
>
> Dear Amber experts,
>
> In this tutorial(https://urldefense.com/v3/__http://ambermd.org/tutorials/advanced/tutorial4/__;!!NVzLfOphnbDXSw!WNyiZy5rfBz6ocXKxtm1HtxODtNPsYgWC5lAPqn32SOF_UE8YSsu1TdRz99lzxy-c1wV$ <https://urldefense.com/v3/__http://ambermd.org/tutorials/advanced/tutorial4/__;!!NVzLfOphnbDXSw!WNyiZy5rfBz6ocXKxtm1HtxODtNPsYgWC5lAPqn32SOF_UE8YSsu1TdRz99lzxy-c1wV$ >), makeDIST_RST can generate sander distance restraint format between two atoms with a 7 colomn input file. May I ask is there a similar script that can generate the sander format of distance restraint between the center of mass of two group of atoms (atoms in each group are from the same residue) automatically by providing similar input as 7col.dist except that 1 residue has a number of atoms in one row?
>
> Many thanks,
> Ming
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