e: How to solve the "LINCS WARNING" problem (Yu Du)
5. atomtype "OE" in charmm36 (Schirra, Simone)
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Message: 1
Date: Fri, 17 Apr 2020 13:30:14 +0900
From: ???
To: gmx-us...@gromacs.org
Subject: Re: [gmx-u
To: gmx-us...@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
re
atomselection for index group of cyclic rings
>> (Prasanth G, Research Scholar)
>> 4. Re: How to solve the "LINCS WARNING" problem (Yu Du)
>> 5. atomtype "OE" in charmm36 (Schirra, Simone)
>>
>>
>> --
>>
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
a, Simone)
>
>
> ----------
>
> Message: 1
> Date: Fri, 17 Apr 2020 13:30:14 +0900
> From: ???
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem
> M
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
t;
> Cheers,
>
> Yu
>
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> on behalf of 변진영
>
> Sent: Thursday, April 16, 2020 21:43
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] How to solve the "LINCS WARN
: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of 변진영
Sent: Thursday, April 16, 2020 21:43
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem
Thank you for reply Du, You
You said that "If you want more suggestion, you need to provi
_
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> on behalf of 변진영
>
> Sent: Tuesday, April 14, 2020 14:32
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] How to solve the "LINCS WARNING" problem
>
> Dear GROMACS users,
: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of 변진영
Sent: Tuesday, April 14, 2020 14:32
To: gmx-us...@gromacs.org
Subject: [gmx-users] How to solve the "LINCS WARNING" problem
Dear GROMACS users,
Since I have run the nvt and npt processes for the protein-ligand i
Dear GROMACS users,
Since I have run the nvt and npt processes for the protein-ligand interaction,
I met the the warning messages below
Step 231785, time 463.57 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000176, max 0.003912 (between atoms 3035 and 3037)
bonds that
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