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

[Harimuthu]

Hello sir,
Sir you are tell to check dihedral angle of amino acid but for me the error
was in water molecules so how to overcome this please help me
With regards

On 22 Oct 2016 4:30 p.m., "Harimuthu"  wrote:

> 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.,  requ...@maillist.sys.kth.se> wrote:
>
>> Send gromacs.org_gmx-users mailing list submissions to
>> gromacs.org_gmx-users@maillist.sys.kth.se
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx
>> -users
>> or, via email, send a message with subject or body 'help' to
>> gromacs.org_gmx-users-requ...@maillist.sys.kth.se
>>
>> You can reach the person managing the list at
>> gromacs.org_gmx-users-ow...@maillist.sys.kth.se
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of gromacs.org_gmx-users digest..."
>>
>>
>> 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 
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Switching Group to Verlet
>> Message-ID:
>> > 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 
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Switching Group to Verlet
>> Message-ID:
>> > ail.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 :
>> > 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
>> >
>> > * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>>
>> --
>>
>> Message: 3
>> Date: Fri, 21 Oct 2016 23:24:28 +0530
>> From: Harimuthu 
>> To: gromacs.org_gmx-users@maillist.sys.kth.se
>> Subject: [gmx-users] Error in mdrun
>> Message-ID:
>> > 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  

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

[Harimuthu]

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., 
wrote:

> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users@maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
> gromacs.org_gmx-users-requ...@maillist.sys.kth.se
>
> You can reach the person managing the list at
> gromacs.org_gmx-users-ow...@maillist.sys.kth.se
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> 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 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Switching Group to Verlet
> Message-ID:
>  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 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Switching Group to Verlet
> Message-ID:
>  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 :
> > 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
> >
> > * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
>
> --
>
> Message: 3
> Date: Fri, 21 Oct 2016 23:24:28 +0530
> From: Harimuthu 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Error in mdrun
> Message-ID:
>  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
>