Dear all,
The problem was related to the intel compiler, not to the input file nor software version.
I have done numerous attempts on diverse machines upon which were installed different amber versione (either gpu and cpu-like)
Apparently, intel/2018.3 is not efficient for amber18.
Now, we have recompiled amber18 with intel/2017.4 and everything work perfectly.
If you need much more information, I gonna ask to the ict center.
Thanks for your kind and prompt support.
V
**********************************************
Vito Genna, PhD
EMBO Long-Term Fellow
Molecular Modeling and Bioinformatics
Institute for Research in Biomedicine (IRB Barcelona)
Parc Centific de Barcelona
C/ Baldiri Reixac 10-12
08028 Barcelona
**********************************************
> On 11 Oct 2018, at 17:48, Matias Machado <mmachado.pasteur.edu.uy> wrote:
>
> Dear Vito,
>
> That's rare...
>
> What is in MG.frcmod? Any chance you are messing up with the solvent parameters?
>
> Best,
>
> Matías
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://pasteur.uy/en/laboratorios-eng/lsbm]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "Vito GENNA" <vito.genna.irbbarcelona.org>
> Para: "david case" <david.case.rutgers.edu>, amber.ambermd.org
> Enviados: Jueves, 11 de Octubre 2018 5:48:44
> Asunto: Re: [AMBER] Water do not see the system....
>
> Goodmorning,
>
> I have just run the 'checkoverlap' command and, as expected there are
> numerous (dozen of hundreds) warnings with value dramatically short.
> .........................................................................................................................
> 2 Warning: Atoms 5115:ARG_312.N and 36285:WAT_8745.H2 are close (0.52)
> 2 Warning: Atoms 5124:ARG_312.HG3 and 63241:WAT_17731.O are close (0.40)
> 2 Warning: Atoms 5124:ARG_312.HG3 and 63243:WAT_17731.H2 are close
> (0.69)
> 2 Warning: Atoms 5176:MET_315.HB2 and 36734:WAT_8895.H1 are close (0.75)
> 2 Warning: Atoms 5224:ALA_318.O and 62866:WAT_17606.O are close (0.66)
> 2 Warning: Atoms 5224:ALA_318.O and 62867:WAT_17606.H1 are close (0.34)
> 2 Warning: Atoms 5228:LYS_319.HA and 62973:WAT_17641.H2 are close (0.58)
> 2 Warning: Atoms 5277:TYR_322.N and 51270:WAT_13740.H2 are close (0.43)
> ................................................................................................................................
>
> I really don't knwo what's going on, the only try remaining is to change
> the machine running the calculation.
> Have you guys got an idea of what is going on?
> This is the *mdinfo*:
> NSTEP = 500000 TIME(PS) = 1000.000 TEMP(K) = 298.00 PRESS =
> 0.0
> Etot = 48357.7411 EKtot = 64961.1600 EPtot =
> -16603.4189
> BOND = 1953.0563 ANGLE = 4708.7175 DIHED =
> 9197.0051
> 1-4 NB = 2989.7399 1-4 EEL = 31153.1436 VDWAALS =
> -2016.9171
> EELEC = -69163.1697 EHBOND = 0.0000 RESTRAINT =
> 4575.0057
> EAMBER (non-restraint) = -21178.4246
> Ewald error estimate: 0.1085E+01
>
> These are few steps from the *output*:
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
> 0.0
> Etot = -32032.5985 EKtot = 0.0000 EPtot =
> -32032.5985
> BOND = 230.1502 ANGLE = 2214.4942 DIHED =
> 8832.3438
> 1-4 NB = 3022.5901 1-4 EEL = 31924.2094 *VDWAALS* =
> -2016.9171
> EELEC = -76239.4690 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.1436E+01
> ------------------------------------------------------------------------------
> NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 147.67 PRESS =
> 0.0
> Etot = 14429.2449 EKtot = 32191.1524 EPtot =
> -17761.9074
> BOND = 2293.4897 ANGLE = 4978.1187 DIHED =
> 9561.7504
> 1-4 NB = 3116.9234 1-4 EEL = 31209.3800 *VDWAALS* =
> -2016.9171
> EELEC = -72596.0372 EHBOND = 0.0000 RESTRAINT =
> 5691.3847
> EAMBER (non-restraint) = -23453.2922
> Ewald error estimate: 0.1254E+01
> ------------------------------------------------------------------------------
> NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 227.30 PRESS =
> 0.0
> Etot = 37405.5600 EKtot = 49548.6882 EPtot =
> -12143.1281
> BOND = 3072.0214 ANGLE = 6129.2122 DIHED =
> 9740.1173
> 1-4 NB = 3146.5469 1-4 EEL = 31001.3755 *VDWAALS* =
> -2016.9171
> EELEC = -71063.0644 EHBOND = 0.0000 RESTRAINT =
> 7847.5801
> EAMBER (non-restraint) = -19990.7082
> Ewald error estimate: 0.1187E+01
> ------------------------------------------------------------------------------
> *VDWAALS *has no fluctuations at all....this made me curious....
>
> V
>
>
>
>
>
>
> On Wed, Oct 10, 2018 at 10:48 PM Vito GENNA <vito.genna.irbbarcelona.org>
> wrote:
>
>> Dear David,
>>
>> Thank you for your prompt reply.
>> Well, I have visually inspected the system by opening, with VMD, the
>> topology and the md.nc file.
>> I will make a try with the command you suggested.
>> The strange parameter in the output is the super-stable (the same value)
>> of the vdw.
>>
>> I’ll get back to you ASAP.
>>
>> Thanks in advance.
>>
>> Vito
>>
>>
>>
>>
>> *Vito Genna, Ph.D*
>> *EMBO Fellow*
>> Scientist
>> Molecular Modelling and Bioinformatics
>> Orozco Lab
>>
>> *Dep. of Structural and Computational Biology*
>> *Institute for Research in Biomedicine (IRB Barcelona)*
>> Parc Científic de Barcelona
>> C/ Baldiri Reixac 10-12
>> 08028 Barcelona
>>
>> P.S. Email written with my IPhone. Sorry for typo.
>>
>> Il giorno 10 ott 2018, alle ore 22:16, David A Case <
>> david.case.rutgers.edu> ha scritto:
>>
>> On Wed, Oct 10, 2018, Vito GENNA wrote:
>>
>> Once i got the system I minimize it and what I note is that water molecules
>>
>> dramatically overlap protein's atoms.
>>
>>
>> What is the evidence that this is happening? Did you visualize the
>> system? Calculate the distance from a given water molecule to a given
>> protein atom? Something else?
>>
>> You can use the "checkoverlap" command in cpptraj to print out all short
>> contacts. There should be very few of these following minimization. It
>> would probably also be more helpful to see the *output* from
>> minimization, rather than the input file.
>>
>> Look carefully at the minimization and heating outputs for evidence of
>> problems. It looks like you have 750 residues in your protein: is that
>> correct? You might try a short calculation on a smaller fragment. I
>> didn't notice anything wrong with your tleap input, but I could be
>> missing something.
>>
>> ....dac
>>
>>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
> --
>
> ***********************************************************************
> *Vito Genna, Ph.D*
> *EMBO Fellow*
>
> *Postoctoral Researcher*
>
> *Molecular Modeling and Bioinformatics*
> *Orozco Lab*
>
> *Institute for Research in Biomedicine (IRB Barcelona)*
>
> *Parc Centific de Barcelona*
>
> *C/ Baldiri Reixac 10-12*
> *08028 Barcelona*
>
> ***********************************************************************
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Received on Thu Oct 11 2018 - 09:00:03 PDT
