[gmx-users] High temperature simulation with GROMOS96 54a7

Dear gmx-users, I have a short question. Did GROMACS recent force field "GROMOS96 54a7 force field" parametrize for high temperature classical MD simulation such as 353 K? Is there any reference paper? Sincerely, Sunita -- Gromacs Users mailing list * Please search the archiv

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 121

chloride solutions at high temperatures and pressures:a simulation study http://www.tandfonline.com/doi/abs/10.1080/08927022.2014.992019?journalCode=gmos20 Thanks. Sunita > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To

Re: [gmx-users] Fwd: Concatenating two trajectories

Thanks for quick response.. I tried trjcat -f 1.xtc 2.xtc -o concatenate.xtc But its not concatenating the two, rather overwriting the 2nd trajectory to 1st one. There should be 1600 frames but output contains only 800 frames. Thanks -- View this message in context: http://gromacs.5086.x6.nabble

Re: [gmx-users] Fwd: Concatenating two trajectories

Hello Venkat, Ya, I am sure that I use 1st.cpt to run next 40 ns job Find below the output of trjcat Summary of files and start times used: FileStart time Time step - complex_prod1_old.xtc0.000 p

Re: [gmx-users] Fwd: Concatenating two trajectories

Hello Venkat, Yeah, I think by default it will give 0 ps as start time for both trajectories and it should be set by user using -settime flag Correct me if I am wrong. Regards -- View this message in context: http://gromacs.5086.x6.nabble.com/Fwd-Concatenating-two-trajectories-tp5015956p5015992

[gmx-users] Protein-Ligand complex Implicit simulation

. Still its giving errorsAnyone please suggest me how to proceed further. Thanks in Advance -- -- SUNITA GUPTA Senior Research Fellow Bioinformatics Centre Jawaharlal Nehru University New Delhi- 110067 Email- sunita@gmail.com -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 133, Issue 107

on 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. Protein-Ligand complex Implic

[gmx-users] Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for 9 atomtypes or they might be negative.

ter(s) missing or negative for atom type 'hn' I don't understand why its again complaining about HA and N2, even if it is present in lig.itp. Kindly guide in tackling this problem. Thanks in advance -- -- SUNITA GUPTA Senior Research Fellow Bioinformatics Centre Jawaharlal Nehru

[gmx-users] Fwd: Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for 9 atomtypes or they might be negative.

-- Forwarded message -- From: sunita gupta Date: Mon, Nov 25, 2013 at 3:23 PM Subject: Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for 9 atomtypes or they might be negative. To: gmx-us...@gromacs.org Hello everyon

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 115, Issue 117

4. Re: (no subject) (Justin Lemkul) >5. Fwd: Can't do GB electrostatics; the implicit_genborn_params > section of the forcefield is missing parameters for 9 atomtypes > or they might be negative. (sunita gupta) > > > -

[gmx-users] Fwd: Concatenating two trajectories

with this method. Best Regards -- SUNITA GUPTA Senior Research Fellow Bioinformatics Centre Jawaharlal Nehru University New Delhi- 110067 Email- sunita@gmail.com -- -- SUNITA GUPTA Senior Research Fellow Bioinformatics Centre Jawaharlal Nehru University New Delhi- 110067 Email

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 120, Issue 95

@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. Cannot write trajectory frame;maybe you are out of disk > space (Andre