[gmx-developers] Re: gmx-developers Digest, Vol 74, Issue 6
Carlo Camilloni
carlo.camilloni at gmail.com
Thu Jun 3 10:56:17 CEST 2010
I meant, "there is a problem in"
int calc_gb_chainrule_sse2_double
Carlo
On 3 Jun 2010, at 10:49, gmx-developers-request at gromacs.org wrote:
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> 1. re: implicit solvent (Carlo Camilloni)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 3 Jun 2010 10:48:56 +0200
> From: Carlo Camilloni <carlo.camilloni at gmail.com>
> Subject: [gmx-developers] re: implicit solvent
> To: gmx-developers at gromacs.org
> Message-ID: <C0F4E9F8-D7E3-4C5E-BD93-84EBE85A0630 at gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Mark,
>
> I send you the same input files that I sent to Per Larsson.
> after the last commits on git the problems still appears
> after more or less 200 steps, always as a big increment
> in "fshift after SR[ 22]".
>
> applying a patch in genborn.c:1562-1563:
>
> nj0 = nl->jindex[ai];
> nj1 = nl->jindex[ai+1];
>
> -->
>
> nj0 = nl->jindex[i];
> nj1 = nl->jindex[i+1];
>
>
> and compiling in double without optimizations,
> all works well. Maybe there is a problem in
>
>
> Regards,
> Carlo
>
> Begin forwarded message:
>
>> From: Carlo Camilloni <carlo.camilloni at gmail.com>
>> Date: 1 June 2010 13:43:45 CEST
>> To: Per Larsson <per.larsson at sbc.su.se>
>> Subject: Re: gmx-developers Digest, Vol 74, Issue 1
>>
>>
>>
>> Hi,
>>
>> this is the system I was using. I have also done some
>> debugging:
>> by using -debug 10 flag in mdrun I got this result in mdrun.debug
>>
>>
>>
>> Increasing GB neighbourlist j size to 3190
>> Increasing GB neighbourlist j size to 7986
>> Increasing GB neighbourlist j size to 18489
>> Increasing GB neighbourlist j size to 41490
>> fshift after SR (45x3):
>> fshift after SR[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> fshift after SR[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> fshift after SR[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> fshift after SR[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>> fshift after ...
>>
>> fshift after SR[ 22]={-3.59985e+269, 7.91323e+269, -1.16757e+270}
>> and all the other 0.00
>>
>> vir_part (3x3):
>> vir_part[ 0]={1.52302e+270, 6.71165e+268, -9.94015e+268}
>> vir_part[ 1]={6.71165e+268, 1.38159e+270, -5.32724e+267}
>> vir_part[ 2]={-9.94015e+268, -5.32724e+267, 1.03656e+270}
>> Guessed pbc = xyz from the box matrix
>> Guessed pbc = xyz from the box matrix
>> constraint virial (3x3):
>> constraint virial[ 0]={-1.06645e+269, -6.31248e+267, 5.52275e+267}
>> constraint virial[ 1]={-6.31248e+267, -1.16995e+269, -5.31208e+267}
>> constraint virial[ 2]={5.52275e+267, -5.31208e+267, -1.01260e+269}
>> dekin (3x3):
>> dekin[ 0]={ -inf, -inf, inf}
>> dekin[ 1]={ -inf, -inf, inf}
>> dekin[ 2]={ inf, inf, -inf}
>> ekin (3x3):
>> ekin[ 0]={ 1.07090e+02, -1.28235e+01, 2.44544e+00}
>> ekin[ 1]={-1.28235e+01, 9.93836e+01, -4.73968e+00}
>> ekin[ 2]={ 2.44544e+00, -4.73968e+00, 8.31171e+01}
>> dekin = -inf, ekin = 289.591 vcm = (37724423208582392295386276764510319211320417140435671882380328320812381594880211169413371
>> 358679334568178120349284174636383420665585500528416721787062413484436933391583994571739322882089364956909490686430616721178287
>> 5654860436192621173254981676957696.0000 31180390611175245501077433199741281911130739631997505115600164449706783479065192251777
>> 314796409899660965811414664650242000195439480951995994394538761200379988057180467500001038548378320832492673848303062076640322
>> 1353454826879291876975370559962480640.0000 -1431266541249085767742382230423258785149802680554631655691802070662038285164031728
>> 191772385960655935292355927541486927054477721966709871891976853820786315670152588754868888831140838914572678663771823871985711
>> 373255227035928103075818815545438543806464.0000)
>>
>>
>>
>>
>> moreover after having take a look at the code in genborn.c it seems to me that fr->invsqrta in not properly initialized before the first step.
>>
>> hope this helps,
>> Regards,
>> Carlo
>>
>> On 1 Jun 2010, at 12:58, Per Larsson wrote:
>>
>>> Hi!
>>>
>>> Could you send me your inputfiles, and I'll have a look at it.
>>> It should work.
>>>
>>> Regards
>>> /Per
>>>
>>>
>>> 1 jun 2010 kl. 12.30 skrev Pär Bjelkmar:
>>>
>>>> Sett detta?
>>>>
>>>> Vidarebefordrat brev:
>>>>
>>>>> Message: 1
>>>>> Date: Tue, 1 Jun 2010 11:35:13 +0200
>>>>> From: Carlo Camilloni <carlo.camilloni at gmail.com>
>>>>> Subject: [gmx-developers] implicit solvent in the git version of
>>>>> gromacs
>>>>> To: gmx-developers at gromacs.org
>>>>> Message-ID: <64B168DC-C53F-406B-BA7B-091B3F243527 at gmail.com>
>>>>> Content-Type: text/plain; charset=us-ascii
>>>>>
>>>>> Dear Gromacs Developers,
>>>>>
>>>>> I am trying to test, without any success, the implicit solvent algorithm implemented in the git version of gromacs.
>>>>> I am using a 16 residue beta-hairpin with the charmm forcefield and all the different implicit algorithm still, ecc.
>>>>> But the system explode within the first steps, while turning-off the gbsa all goes well.
>>>>>
>>>>> pbc=no
>>>>> electrostatic=reaction-field-zero or cut-off
>>>>> vdw=shift or cut-off
>>>>> dt=0.002 or 0.001
>>>>> constraint=lincs
>>>>> nstlist=1
>>>>> rlist=rgblist=2
>>>>> both with temperature coupling as without.
>>>>>
>>>>> Is the algorithm still broken?
>>>>>
>>>>> Best regards,
>>>>> Carlo Camilloni
>>>>
>>>
>>
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