[gmx-users] Amber14SB
Alessandra Villa
alessandra.villa.biosim at gmail.com
Thu Mar 5 10:23:57 CET 2020
Hi,
Here a page of force field in GROMACS
http://manual.gromacs.org/documentation/current/user-guide/force-fields.htm
maybe it helps. I did not fully understand your question
Best regards
Alessandra
On Tue, Mar 3, 2020 at 10:04 AM Eduardo Mayo <eduardomayoyanes at gmail.com>
wrote:
> 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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