Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 172, Issue 89

[Dan Gil]

I think that may indicate that their is something wrong with your input
files, possibly the configuration.

Did you check if the configuration has any bad contacts?

On Wed, Aug 29, 2018 at 7:15 AM sagar bathla  wrote:

> hi Dan,
>
> I got the warnings at the start of the mdrun.
>
> Regards
> Sagar
>
> On Wed, Aug 29, 2018 at 3:30 PM <
> gromacs.org_gmx-users-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. free energy of complex system (abhisek Mondal)
> >2.  restrain ligand in free energy. (T?ng Ho?ng)
> >3. Re: rotation of atoms by more than 90 degrees & LINCS
> >   Warnings (Dan Gil)
> >4. Re: rotation of atoms by more than 90 degrees & LINCS
> >   Warnings (Dan Gil)
> >
> >
> > --
> >
> > Message: 1
> > Date: Wed, 29 Aug 2018 11:23:16 +0530
> > From: abhisek Mondal 
> > To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] free energy of complex system
> > Message-ID:
> >  > f3+ulyykpn2zi3xg38dctm...@mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hi,
> > I'm just trying to calculate free energy of a complex system using
> > following method:
> >
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html
> >
> > However, I'm facing some difficulties understanding how can I achieve the
> > goal. The tutorial goes on with a single entity from lambda=0 to 1 with
> > 0.05 spacing for data collection.
> >
> > Now, if I would like to calculate free energy of a complex (say, dimeric
> > protein) then how am I supposed to design the lambda states ?
> > I mean will it be like, one monomer will remain constant and the other
> > monomer goes from lambda=0 to 1 state ? If that be the case then please
> > suggest a way to customize the procedure.
> >
> > Please provide some suggestions.
> > I'm really willing to apply this method in my scenario.
> > Thank you.
> > --
> > Abhisek Mondal
> >
> > *Senior Research Fellow*
> > *Protein Crystallography Group*
> >
> > *Structural Biology and Bioinformatics Division*
> > *CSIR-Indian Institute of Chemical Biology*
> >
> > *Kolkata 700032*
> >
> > *INDIA*
> >
> >
> > --
> >
> > Message: 2
> > Date: Wed, 29 Aug 2018 14:06:31 +0700
> > From: T?ng Ho?ng 
> > To: gmx-us...@gromacs.org
> > Subject: [gmx-users]  restrain ligand in free energy.
> > Message-ID:
> > <
> > cafn5yuf4myt_q-xfn5qkdavn25oouj4srw-bele21grnoyk...@mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hello everyone,
> > i am trying to calculate free energy for complex protein-ligand. but in
> > tutorial it just have methane in water. So i find this
> >
> http://www.alchemistry.org/wiki/Absolute_Binding_Free_Energy_-_Gromacs_2016
> > but the problem is i don know how to restrain this ligand.
> > in file complex.top i see that intramolecular - interaction , bond,
> angle ,
> > diheral.  and in .mdp file i see bonds_lambda increase.  I wonder how i
> can
> > restrain like this . where i can find intramolecular -interaction/
> > Thank you for your help.
> >
> > Regrads,
> > Tung,
> >
> > --
> > Ho?ng T?ng / student
> > hoangtung9...@gmail.com / +(84) 0928 478 789
> >
> > University of Medicine and Pharmacy I Ho Chi Minh City
> > 197 Nguyen Thai Hoc, Pham Ngu Lao, District 1, HCM City
> > 
> >
> > [image: Facebook]   [image: Skype]
> > 
> >
> >
> > --
> >
> > Message: 3
> > Date: Wed, 29 Aug 2018 05:56:14 -0400
> > From: Dan Gil 
> > To: gmx-us...@gromacs.org
> > Cc: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: Re: [gmx-users] rotation of atoms by more than 90 degrees &
> > LINCS   Warnings
> > Message-ID:
> >  > hog...@mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hi Sagar,
> >
> > At which time step do you get LINCS warnings?
> >
> > Also, please see:
> >
> http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
> >
> > Dan
> >
> > On Tue, Aug 28, 2018 at 3:19 AM sagar bathla 
> > wrote:
> >
> > > Dear all,
> > >
> > > My system consists of 2 orthorhombic parallel graphene sheets in a big
> > > 

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 172, Issue 89

[sagar bathla]

hi Dan,

I got the warnings at the start of the mdrun.

Regards
Sagar

On Wed, Aug 29, 2018 at 3:30 PM <
gromacs.org_gmx-users-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. free energy of complex system (abhisek Mondal)
>2.  restrain ligand in free energy. (T?ng Ho?ng)
>3. Re: rotation of atoms by more than 90 degrees & LINCS
>   Warnings (Dan Gil)
>4. Re: rotation of atoms by more than 90 degrees & LINCS
>   Warnings (Dan Gil)
>
>
> --
>
> Message: 1
> Date: Wed, 29 Aug 2018 11:23:16 +0530
> From: abhisek Mondal 
> To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] free energy of complex system
> Message-ID:
>  f3+ulyykpn2zi3xg38dctm...@mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
> I'm just trying to calculate free energy of a complex system using
> following method:
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html
>
> However, I'm facing some difficulties understanding how can I achieve the
> goal. The tutorial goes on with a single entity from lambda=0 to 1 with
> 0.05 spacing for data collection.
>
> Now, if I would like to calculate free energy of a complex (say, dimeric
> protein) then how am I supposed to design the lambda states ?
> I mean will it be like, one monomer will remain constant and the other
> monomer goes from lambda=0 to 1 state ? If that be the case then please
> suggest a way to customize the procedure.
>
> Please provide some suggestions.
> I'm really willing to apply this method in my scenario.
> Thank you.
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
> *Protein Crystallography Group*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
>
>
> --
>
> Message: 2
> Date: Wed, 29 Aug 2018 14:06:31 +0700
> From: T?ng Ho?ng 
> To: gmx-us...@gromacs.org
> Subject: [gmx-users]  restrain ligand in free energy.
> Message-ID:
> <
> cafn5yuf4myt_q-xfn5qkdavn25oouj4srw-bele21grnoyk...@mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello everyone,
> i am trying to calculate free energy for complex protein-ligand. but in
> tutorial it just have methane in water. So i find this
> http://www.alchemistry.org/wiki/Absolute_Binding_Free_Energy_-_Gromacs_2016
> but the problem is i don know how to restrain this ligand.
> in file complex.top i see that intramolecular - interaction , bond, angle ,
> diheral.  and in .mdp file i see bonds_lambda increase.  I wonder how i can
> restrain like this . where i can find intramolecular -interaction/
> Thank you for your help.
>
> Regrads,
> Tung,
>
> --
> Ho?ng T?ng / student
> hoangtung9...@gmail.com / +(84) 0928 478 789
>
> University of Medicine and Pharmacy I Ho Chi Minh City
> 197 Nguyen Thai Hoc, Pham Ngu Lao, District 1, HCM City
> 
>
> [image: Facebook]   [image: Skype]
> 
>
>
> --
>
> Message: 3
> Date: Wed, 29 Aug 2018 05:56:14 -0400
> From: Dan Gil 
> To: gmx-us...@gromacs.org
> Cc: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] rotation of atoms by more than 90 degrees &
> LINCS   Warnings
> Message-ID:
>  hog...@mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Sagar,
>
> At which time step do you get LINCS warnings?
>
> Also, please see:
> http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
>
> Dan
>
> On Tue, Aug 28, 2018 at 3:19 AM sagar bathla 
> wrote:
>
> > Dear all,
> >
> > My system consists of 2 orthorhombic parallel graphene sheets in a big
> > triclinic box filled with water. when i am trying to run equillibration
> > then i am getting too many lincs warnings and simulation has been getting
> > crashed everytime. i have put retraint on all atoms of graphene but still
> > this problem is occuring again.
> >
> > My .mdp file looks like this
> > title   = OPLS Graphene IN WATER NVT equilibration
> > define  = -DPOSRES -DFLEXIBLE   ; position restrain the protein
> >
> > ; Run parameters
> > integrator  = md; leap-frog