[gmx-users] gromacs.org_gmx-users Digest, Vol 150, Issue 98

Harimuthu mmddharimuthu at gmail.com
Sat Oct 22 13:01:02 CEST 2016 

Sir I have used opls forcefield and showing such a errors
And this is the first time I am getting such a error

On 22 Oct 2016 3:30 p.m., <gromacs.org_gmx-users-request at maillist.sys.kth.se>
wrote:

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> Today's Topics:
>
>    1. Re: Switching Group to Verlet (Mahmood Naderan)
>    2. Re: Switching Group to Verlet (Mario Fern?ndez Pend?s)
>    3. Error in mdrun (Harimuthu)
>    4. D-amino acids' force fields (Mijiddorj Batsaikhan)
>    5. Re: D-amino acids' force fields (Tsjerk Wassenaar)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 21 Oct 2016 18:03:42 +0330
> From: Mahmood Naderan <mahmood.nt at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Switching Group to Verlet
> Message-ID:
>         <CADa2P2WckUZiLUHXf7MAf_4boNmevX-AEXM95injmUHWqoA8Dw@
> mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> One more question.
> Currently, gromacs prints the output on every step!
>
> Step=  159, Dmax= 3.8e-03 nm, Epot= -8.39592e+05 Fmax= 2.45536e+03, atom=
> 2111
> Step=  160, Dmax= 4.6e-03 nm, Epot= -8.39734e+05 Fmax= 4.30685e+03, atom=
> 2111
> Step=  161, Dmax= 5.5e-03 nm, Epot= -8.39913e+05 Fmax= 3.78613e+03, atom=
> 2111
>
> Can you please tell me how to increase the print step? What is the
> appropriate switch for that?
>
>
> Regards,
> Mahmood
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 21 Oct 2016 15:46:25 +0100
> From: Mario Fern?ndez Pend?s <mariofp77 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Switching Group to Verlet
> Message-ID:
>         <CA+ag3a7h2+THdRoJXo4U_SK=fwPV8mK4j64zNkbtiEiGZMGeHQ at mail.
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Mahmood,
>
> I always find very useful this page:
> http://manual.gromacs.org/online/mdp_opt.html
>
> For your particular case I think you should look at
> http://manual.gromacs.org/online/mdp_opt.html#out
>
> Cheers,
> Mario
>
> 2016-10-21 15:33 GMT+01:00 Mahmood Naderan <mahmood.nt at gmail.com>:
> > One more question.
> > Currently, gromacs prints the output on every step!
> >
> > Step=  159, Dmax= 3.8e-03 nm, Epot= -8.39592e+05 Fmax= 2.45536e+03, atom=
> > 2111
> > Step=  160, Dmax= 4.6e-03 nm, Epot= -8.39734e+05 Fmax= 4.30685e+03, atom=
> > 2111
> > Step=  161, Dmax= 5.5e-03 nm, Epot= -8.39913e+05 Fmax= 3.78613e+03, atom=
> > 2111
> >
> > Can you please tell me how to increase the print step? What is the
> > appropriate switch for that?
> >
> >
> > Regards,
> > Mahmood
> > --
> > Gromacs Users mailing list
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>
> ------------------------------
>
> Message: 3
> Date: Fri, 21 Oct 2016 23:24:28 +0530
> From: Harimuthu <mmddharimuthu at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Error in mdrun
> Message-ID:
>         <CAP_Jo1Yzrq_iaDHLFosEd+c3CXxpKurquM64gJUfNAmmZn2y7A@
> mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> hello sir
>
> While running the protein in water energy minimisation
> gmx mdrun -v -deffnm em
> an error is occurred as follows
>
> Program gmx mdrun, VERSION 5.1.2
> Source code file:
> /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line:
> 555
>
> Fatal error:
>
> step 14: Water molecule starting at atom 8686 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> in that i searched the error in input file which was in 8686 atom and found
> a error in coordinate value of water it was as
> ATOM   8686  OW  SOL  1551       0.823  30.858  10.228  1.00
> 0.00
> ATOM   8687  HW1 SOL  1551       0.825  31.173  11.177  1.00
> 0.00
> ATOM   8688  HW2 SOL  1551      95.631  30.777   9.906  1.00  0.00
>
> in this the third atom X coordinate is 95.631 and i changed it into 0.631 i
> dont know whether to relible or no, if i do potential graph it is good to
> see, so can anyone help me in solving this problem
> With regards
> Harimuthu
>
>
> ------------------------------
>
> Message: 4
> Date: Sat, 22 Oct 2016 14:09:45 +0900
> From: Mijiddorj Batsaikhan <b.mijiddorj at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] D-amino acids' force fields
> Message-ID:
>         <CABgRApvLuvCFQeo_HMwaB_OTxerDrOK4W1Te_umf=RX9uingbA@
> mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear users,
>
> Hello, Is there any force field that contains parameters of D-amino acids?
> In my case I need to D-ILE and D-Phe amino acids simulation. Please, advice
> me.
>
> Best regards,
>
> Mijiddorj
>
>
> ------------------------------
>
> Message: 5
> Date: Sat, 22 Oct 2016 10:11:50 +0200
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] D-amino acids' force fields
> Message-ID:
>         <CABzE1Sh3MgjP8puni4mF9sk720JjaAyxaZZGg0W55vHiDaS4sA at mail.
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Mijidorj,
>
> These amino acids are chemically and topologically equivalent to their L
> counterparts. For united atom force fields you only need to invert the
> improper dihedral at the C-alpha. For atomistic force fields you don't need
> to change anything, except the CMAP stuff in Charmm for the backbone
> dihedral, and you need to reset the hydrogen position if you used pdb2gmx
> for building the topology and the hydrogens.
>
> Cheers,
>
> Tsjerk
>
> On Oct 22, 2016 8:03 AM, "Mijiddorj Batsaikhan" <b.mijiddorj at gmail.com>
> wrote:
>
> > Dear users,
> >
> > Hello, Is there any force field that contains parameters of D-amino
> acids?
> > In my case I need to D-ILE and D-Phe amino acids simulation. Please,
> advice
> > me.
> >
> > Best regards,
> >
> > Mijiddorj
> > --
> > Gromacs Users mailing list
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> > * Please search the archive at http://www.gromacs.org/
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> >
>
>
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> End of gromacs.org_gmx-users Digest, Vol 150, Issue 98
> ******************************************************
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