[gmx-developers] re: implicit solvent

[Carlo Camilloni]

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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