[gmx-users] Amber14SB

Eduardo Mayo eduardomayoyanes at gmail.com
Tue Mar 3 10:02:56 CET 2020 

Hi!!
I'm sorry if is the amber14sb poster on the gromacs download site good??
I've seen the warning on the page and I don't know what to think.
Thanks in advance.

On Mon, Mar 2, 2020, 3:38 PM <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

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> Today's Topics:
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>    1. Re: install and mdrun problems (Bogdanov, Vladimir)
>    2. sadaf rani shared "dihedral_angles" with you
>       (sadaf rani (via Dropbox))
>    3. regarding dihedral restraints (Sadaf Rani)
>    4. Fwd: regarding dihedral restraints (Sadaf Rani)
>    5. Re: grompp error : Atomtype CAro not found (Dallas Warren)
>
>
>
> ---------- Forwarded message ----------
> From: "Bogdanov, Vladimir" <bogdanov.7 at osu.edu>
> To: Kunal Dutta <mamapcr at gmail.com>, "gmx-users at gromacs.org" <
> gmx-users at gromacs.org>
> Cc: "gromacs.org_gmx-users at maillist.sys.kth.se" <
> gromacs.org_gmx-users at maillist.sys.kth.se>
> Bcc:
> Date: Mon, 2 Mar 2020 16:36:59 +0000
> Subject: Re: [gmx-users] install and mdrun problems
> Hi Kunal,
>
> Asus TUF X299 Mark2, Intel I7-7820x, Nvidia Titan Xp, Crucial Ballistix
> Sport LT 2666 MHz 128GB, Samsung 970 EVO 500GB NVMe PCIe M.2, Samsung SSD
> 860 EVO 2TB SATA III, Corsair Hydro Series H100i v2 AIO Liquid CPU Cooler.
>
> It looks like the reason of my PC shut down is lying in the Bios settings,
> but I don't know the version of BIOS, I can look it later, if you need.
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Kunal
> Dutta <mamapcr at gmail.com>
> Sent: Monday, March 2, 2020 8:56 AM
> To: gmx-users at gromacs.org <gmx-users at gromacs.org>
> Cc: gromacs.org_gmx-users at maillist.sys.kth.se <
> gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] install and mdrun problems
>
> Hello Sir,
> May I know the detailed configuration of your system.
> Sincerely,
> Kunal
>
>
>
>
> On Mon, 2 Mar 2020 at 09:08, Bogdanov, Vladimir <bogdanov.7 at osu.edu>
> wrote:
>
> > Hi all,
> >
> > I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2),
> but
> > when I did make check, my PC turned off. I also tried to install
> > Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I
> tried
> > to do mdrun, my PC also shut down. I also tried the following
> combination:
> > nvidia-smi 440.59, CUDA 9.2.
> >
> > Any ideas would be helpful.
> >
> > Thanks,
> > Vlad
> > --
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> ---------- Forwarded message ----------
> From: "sadaf rani (via Dropbox)" <no-reply at dropbox.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Cc:
> Bcc:
> Date: Mon, 2 Mar 2020 17:41:36 +0000
> Subject: [gmx-users] sadaf rani shared "dihedral_angles" with you
> Hi Nikhil,
>
> sadaf rani (sadafrani6 at gmail.com) invited you to view the folder "
> dihedral_angles " on Dropbox.
>
> sadaf said:
> "Dihedral angles graphs"
>
> Go to folder[1]
>
> Enjoy!
> The Dropbox team
>  sadaf and others will be able to see when you view files in this folder.
> Other files shared with you through Dropbox may also show this info. Learn
> more[2] in our help center.
>
> [1]: https://www.dropbox.com/l/scl/AACA-vmaSSldqrMmtwPiRsCZm4gGyXu3HHY
> [2]: https://www.dropbox.com/l/AAB8qx9y7zEdVmqC5iR2EtvSb49UsMPBKQk
>
>
>
> ---------- Forwarded message ----------
> From: Sadaf Rani <sadafrani6 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Cc:
> Bcc:
> Date: Mon, 2 Mar 2020 17:42:19 +0000
> Subject: [gmx-users] regarding dihedral restraints
> Dear Gromacs users
> I am restraining three dihedral angles between atoms of two
> different residues. when I measure it using the following command:-
>
> gmx angle -type dihedral -f md_prod.xtc -n dihedral.ndx -ov group.xvg -of
> trans.xvg
>
> I am getting one of my dihedrals graphs as mentioned in the link.
> https://www.dropbox.com/home/dihedral_angles
> My dihedral angles have a multiplicity of 1 as mentioned below:-
> [ dihedral_restraints ]
> ;   ai    aj    ak    al   type   phiA     dphiA    fcA     phiB    dphiB
>   fcB
>     72    74    31    33   1     146.72     0.0     0   146.72     0.0
> 41.840
>     75    74 31    27   1     173.10     0.0     0   173.10     0.0
>  41.840
>     75    74 31    25   1     158.21     0.0     0   158.21     0.0
>  41.840
>
>  However, in gromacs manual, I read this:-
>
>
> *Counting transitions only works for dihedrals with multiplicity 3*
> Am I doing something wrong?  How should I measure dihedral restraint over
> time?
>
> Thanks.
>
> Sadaf
>
>
>
>
> ---------- Forwarded message ----------
> From: Sadaf Rani <sadafrani6 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Cc:
> Bcc:
> Date: Mon, 2 Mar 2020 17:43:55 +0000
> Subject: [gmx-users] Fwd: regarding dihedral restraints
> Dear Gromacs users
> I am restraining three dihedral angles between atoms of two
> different residues. when I measure it using the following command:-
>
> gmx angle -type dihedral -f md_prod.xtc -n dihedral.ndx -ov group.xvg -of
> trans.xvg
>
> I am getting one of my dihedrals graphs as mentioned in the link.
> https://www.dropbox.com/sh/1ff45is9412dld4/AACDXjV0T47P01RgCJ1Baccca?dl=0
> My dihedral angles have a multiplicity of 1 as mentioned below:-
> [ dihedral_restraints ]
> ;   ai    aj    ak    al   type   phiA     dphiA    fcA     phiB    dphiB
>   fcB
>     72    74    31    33   1     146.72     0.0     0   146.72     0.0
> 41.840
>     75    74 31    27   1     173.10     0.0     0   173.10     0.0
>  41.840
>     75    74 31    25   1     158.21     0.0     0   158.21     0.0
>  41.840
>
>  However, in gromacs manual, I read this:-
>
>
> *Counting transitions only works for dihedrals with multiplicity 3*
> Am I doing something wrong?  How should I measure dihedral restraint over
> time?
>
> Thanks.
>
> Sadaf
>
>
>
>
> ---------- Forwarded message ----------
> From: Dallas Warren <dallas.warren at monash.edu>
> To: GROMACS users <gmx-users at gromacs.org>
> Cc:
> Bcc:
> Date: Tue, 3 Mar 2020 07:36:56 +1100
> Subject: Re: [gmx-users] grompp error : Atomtype CAro not found
> You need to use the same forcefield.
>
> Since you are using ATB to generate the topology for your small molecule,
> then it stands to reason that you then should use ATB for the lipid
> molecule.
>
> Search ATB, I'm pretty sure the various lipids will already be there, and
> suspect they will be some that the developers of the forcefield added
> themselves, rather than a user submitting.
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On Mon, 2 Mar 2020 at 18:40, Atila Petrosian <atila.petrosian at gmail.com>
> wrote:
>
> > Hi Dallas,
> > thanks for your answer. I saw README file in gromos54a7_atb.ff from ATB
> > server.
> >
> > My system contains lipid molecules and small molecule. For lipid
> molecules,
> > Justine Lemkul suggested to use gromos53a6_lipid.ff. How to use both
> > of gromos54a7_atb.ff
> > and  gromos53a6_lipid.ff in topology file.
> >
> > Please guide me.
> >
> > Best,
> > Atila
> > --
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