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

Harimuthu mmddharimuthu at gmail.com
Sat Oct 22 14:39:29 CEST 2016 

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" <mmddharimuthu at gmail.com> 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., <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 at 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.gm
>> 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 <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
>> >
>> > * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>> >
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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 at 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 at 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.gm
>> ail.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
>> >
>> > * 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-request at gromacs.org.
>> >
>>
>>
>> ------------------------------
>>
>> --
>> Gromacs Users mailing list
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>> * Please search the archive at http://www.gromacs.org/Support
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>> End of gromacs.org_gmx-users Digest, Vol 150, Issue 98
>> ******************************************************
>>
>

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