If your data isn't confidential could you send me your inputs or an example system? I can take a look at this later in the week.
My initial guesses are that the code might be using the imaged atom coordinates, so if molecules wrap, then it might be greatly changing the CoM that it uses to determine the restraints, this would explain why during earlier time steps the code works fine but over long distances issues occur. It would also explain why smaller atom sets might not see this issue.
Sorry that the restraints code has been causing such a headache.
Thanks,
Charlie
On 3/10/19, 7:19 PM, "Pratul Agarwal" <pratul.agarwal-lab.org> wrote:
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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