[gmx-users] How to solve the "LINCS WARNING" problem

[Yu Du]

Hi Jinyoung,

I'm glad to hear that you have found the problem. You can always use grompp to check your topology of the whole system. If you want to understand the GROMACS topology, check Chapter 5. Topologies in GROMACS Manual.

Words in the end: If you have mastered the basic process of protein-ligand simulation with GROMOS ff, you probably wander why we droped GROMOS ff and use others (https://redmine.gromacs.org/issues/2884).

Bye,
Yu
________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of 변진영 <byunjy0614 at gmail.com>
Sent: Monday, April 20, 2020 15:27
To: gmx-users at gromacs.org <gmx-users at gromacs.org>
Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem

Hi Yu

I simulated the both case (1), (2) for only all-atom ligand system and only protein system respectively you mentioned.
I run the each case; the NVT and NPT equilibration with 200ps and 1ns respectively. And there are no problems during NVT and NPT equilibration.

And while I wrote the ligand only topology file, I realized that there is specific order in writing topology file (before I don’t exactly know about the order.)

Below is the last section of  my topology file:

 ; Include Position restraint file
#ifdef POSRES
#include "../PROTEIN/posre.itp"
#endif

#include "../LIGAND/lig.itp"

#ifdef POSRES_LIG
#include "../LIGAND/lig_posre.itp"
#endif


; Include water topology
#include "gromos54a7_atb_lipid.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include topology for ions
#include "gromos54a7_atb_lipid.ff/ions.itp"

[ system ]
; Name
--- in water

[ molecules ]
; Compound        #mols
Protein_chain_A     1
LIG                 1
SOL         30059
NA               4

—————————————————————————————————————

Is there any problem with my topology file and Is it the right order?

Thank you very much b, You

> 2020. 4. 17. 오후 3:34, Yu Du <ydu-sci at outlook.com> 작성:
>
> Hi Jinyoung,
>
> You made it clear.
>
> If you do not have special needs in all-atom version of the ligand, you can also try the united-atom topology of the very same ligand.
>
> To check the origin of LINCS WARNING, I suggest running MD simulation with only protein and only ligand in the same process you followed in a divide and conquer strategy.
>
> Could you run the following simulation to pinpoint the error?
>
> (1) Simulation only all-atom ligand in the system.
> (2) Simulation only protein in the system.
> (3) Simulation only united-atom ligand in the system if it's possible.
>
> In the end, I noticed that you used ATB topology, so you need to strictly follow the instruction in the ATB ff file folders for protein-ligand simulation.
>
> PS: gmx-users mail list do not receive attachment.
>
> Cheers,
> Yu
>
> --
> 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

* 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.