Thanks for the information. My files has less than 200 groups (atoms).
PS: ntpr and ntwe are artificially set = 1 for debugging purposes. In
production run, = 1000 is used.
--- input file ---
&cntrl
imin=0, irest=1, ntx=5, nmropt=1,
ntt=0, tempi=300.0 ,temp0=300.0, tautp=1.0,
ntb=1, ntc=2, ntf=2, tol=0.000001,
nstlim=10000, dt=0.001,
ntpr=1, ntwr=10000, ntwx=10000, ntwe=1,
cut=10.0, iwrap=1, ntr=0,
/
&ewald
dsum_tol=0.000001,
/
&wt type='DUMPFREQ', istep1=100, &end
&wt type='END' &end
DISANG=RST
DUMPAVE=dumpave
--- RST ---
&rst
iat=-1,-1,
iresid=0,
igr1=186,187,188,189,190,191,192,193,194,195,196,
614,615,616,617,618,619,620,621,622,623,624,625,626,627,628,629,
1774,1775,1776,1777,1778,1779,1780,1781,1782,1783,1784,1785,0,
igr2=1923,1924,1925,1926,1927,1928,1929,1930,1931,1932,1933,1934,
1935,1936,1937,1938,1939,1940,1941,1942,1943,1944,1945,1946,1947,1948,1949,
1950,1951,1952,1953,1954,1955,1956,1957,1958,1959,1960,1961,1962,1963,1964,
r1=0.0, r2=4, r3=4, r4=99.9,
rk2=1.5, rk3=1.5,
&end
&rst
iat=-1,-1,
iresid=0,
igr1=186,187,188,189,190,191,192,193,194,195,196,
614,615,616,617,618,619,620,621,622,623,624,625,626,627,628,629,
1774,1775,1776,1777,1778,1779,1780,1781,1782,1783,1784,1785,0,
igr2=1858,1859,1860,1861,1862,1863,1864,1865,1866,1867,1868,1869,1870,1871,1872,1873,
1874,1875,1876,1877,1878,1879,1880,1881,1882,1883,1884,1885,1886,1887,1888,1889,1890,1891,
r1=0.0, r2=4, r3=4, r4=99.9,
rk2=1.5, rk3=1.5,
&end
Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)
Web: http://www.agarwal-lab.org/
On 3/10/2019 4:44 PM, Kellon Belfon wrote:
> Hi Pratul,
>
> The maximum number of atoms in a COM group is capped at 200 atoms. It is a
> hardcoded limit in pmemd (maxigr=1024).
>
> It will also be helpful if you share your input files.
>
> On Sun, Mar 10, 2019 at 3:11 PM Stephan Schott <schottve.hhu.de> wrote:
>> Seems to be related to: http://archive.ambermd.org/201903/0056.html
>>
>> El dom., 10 mar. 2019 a las 19:51, Pratul Agarwal (<pratul.agarwal-lab.org
>> )
>> escribió:
>>
>>> Is there a limit for number of atoms that can be included in group(s)
>>> while using COM restraints with pmemd.cuda v18?
>>>
>>> I am seeing significant divergence in restraint energy term between CPU
>>> and GPU version, for groups with about 50 atoms. For smaller groups
> with
>>> ~20 atoms, GPU simulations appear to be stable and comparable to CPU
>>> version. However, for groups with ~50 atoms the restraint energy term is
>>> showing "*********" within ~2000 steps (= 4 ps), while CPU simulations
> are
>>> stable for same input.
>>>
>>> All patches have been applied including the relevant patch.7. Any
> pointers
>>> will be highly appreciated, and I am happy to provide more details.
>>>
>>> --
>>> Pratul K. Agarwal, Ph.D.
>>> (Editorial Board Member: PLoS ONE, Microbial Cell Factories)
>>> Web: http://www.agarwal-lab.org/
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>> --
>> Stephan Schott Verdugo
>> Biochemist
>>
>> Heinrich-Heine-Universitaet Duesseldorf
>> Institut fuer Pharm. und Med. Chemie
>> Universitaetsstr. 1
>> 40225 Duesseldorf
>> Germany
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> --
> Kellon A. A. Belfon, Graduate Student
> Carlos Simmerling Laboratory
> The Laufer Center for Physical and Quantitative Biology
> The Department of Chemistry, Stony Brook University
> Stony Brook, New York 11794
> Phone: (347) 546-4237 Email: kellon.belfon.stonybrook.edu
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Received on Sun Mar 10 2019 - 16:30:02 PDT
