Re: [gmx-users] amber99bsc0 force field

No, but you can download it from the user contributions part of the GROMACS website: http://www.gromacs.org/Downloads/User_contributions/Force_fields Cheers Tom From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se

Re: [gmx-users] syntax for gmx distance

Thanks Teemu, That was spot on. I simply took the -select argument and dropped it into a text file then used the -sf option instead. Works perfectly. Thanks again Anthony On 14/09/2015 12:34, "Nash, Anthony" wrote: >Thanks Teemu, > >I’ll look into this further. > >Thanks

Re: [gmx-users] problem implementing REST2 in GROMACS 4.6.5

Hi, The mdrun .log file should be emitting the same energy values on the two replicas as are used in the exchange attempt. Is that what you are comparing when you say "I have also calculated..." If mdrun's potential energy output is the same on each replica, then the problem likely lies with your

Re: [gmx-users] struggles with cyclic peptides

On 9/14/15 6:58 AM, Nikhil wrote: Hi Justin, So your saying working with Gromacs for cyclic peptide is hopeless using available methods? I don't see a way to do it. i tried all terminals in .tdb file removing C ,O and H from -COOH so that only O will add up and before that removing O

Re: [gmx-users] grompp error

On 9/14/15 4:30 AM, faride badalkhani wrote: Dear GROMACS users, I need to simulate a hyper branched polymer (a polyamidoamine dendrimer). I used the GROMOS53A6 to perform the simulation. But, I have a problem with defining the angles and dihedrals that are between two residues (because of

Re: [gmx-users] amber99bsc0 force field

On 9/14/15 6:02 AM, Andrew Bostick wrote: Dear all Is there amber99bsc0 in gromacs default force fields? Not by default. But the files are available at: http://www.gromacs.org/Downloads/User_contributions/Force_fields Anything downloaded from that page is unofficial, but usually work

[gmx-users] GROMACS 5 paper, out now!

Hi GROMACS people, There's a new GROMACS paper now in press, published in the first issue of the new software-focused journal called SoftwareX. The journal is open access, and our work can be found at http://dx.doi.org/10.1016/j.softx.2015.06.001 Please read, and please cite in your work using

Re: [gmx-users] struggles with cyclic peptides

Hi Justin, So your saying working with Gromacs for cyclic peptide is hopeless using available methods? i tried all terminals in .tdb file removing C ,O and H from -COOH so that only O will add up and before that removing O from the pdb ,i tired that but ends up with lots of errors. i found

Re: [gmx-users] syntax for gmx distance

On 9/14/15 6:29 AM, Nash, Anthony wrote: > Just downloaded the .tpr and .trr to my machine and tried exactly the same > command: > > gmx distance -n index.ndx -f umb_1_all.trr -s umb_1_umb.tpr -oh > umb_1_distance_hist.xvg -oall umb_1_distance.xvg -select 'com of group > "ZINC" plus com of

[gmx-users] Using TIP4P(2005) with GROMOS-53a6

Hello users, I am simulating a polymer in TIP4P(2005) water with GROMOS53a6 as the force field. I am using the same mdp options as has been provided in the source website. The following error shows up: " Molecule type 'SOL' has 6 constraints. For stability and efficiency there should not be

[gmx-users] Lowering Torsional barrier for conformational sampling

Hello, I was wondering if there is an option in GROMACS to reduce the dihedral energy barrier of a bond (in a small molecule) to promote greater conformational sampling during a MD simulation? Any help is much appreciated. Thanks, Andy -- Gromacs Users mailing list * Please search the

Re: [gmx-users] Lowering Torsional barrier for conformational sampling

Hi, Not yet AFAIK, but people tend to use tools like PLUMED to help out with this. Mark On Mon, Sep 14, 2015 at 4:19 PM Arjun Kalra wrote: > Hello, > > I was wondering if there is an option in GROMACS to reduce the dihedral > energy barrier of a bond (in a small molecule)

Re: [gmx-users] miscelle formation using ligands only

i tried to prepare a topolgy file for my ligands and it contained following things, #include "gromos43a1.ff/forcefield.itp" #include "drg1.itp" #include"drg2.itp" #include"drg3.itp" #include "gromos43a1.ff/spc.itp" [system] miscelle [molecules] drg18 drg2 5 drg3 7 sol

Re: [gmx-users] Using TIP4P(2005) with GROMOS-53a6

Furthermore, G53a6 (even with SPC) is problematic for helices in proteins. I would advise you to use the more recent G54a7. João On Mon, Sep 14, 2015 at 3:11 PM, Justin Lemkul wrote: > > > On 9/14/15 10:05 AM, Pallavi Banerjee wrote: > >> Thanks for your reply, Micholas. >>

Re: [gmx-users] miscelle formation using ligands only

What does the first line of drg1.itp look like? On Monday, September 14, 2015, Chetan Puri wrote: > i tried to prepare a topolgy file for my ligands and it contained following > things, > #include "gromos43a1.ff/forcefield.itp" > #include "drg1.itp" > #include"drg2.itp" >

Re: [gmx-users] miscelle formation using ligands only

On 9/14/15 11:18 AM, Chetan Puri wrote: i tried to prepare a topolgy file for my ligands and it contained following things, #include "gromos43a1.ff/forcefield.itp" #include "drg1.itp" #include"drg2.itp" #include"drg3.itp" #include "gromos43a1.ff/spc.itp" [system] miscelle [molecules] drg1

Re: [gmx-users] Stampede multiple gpu nodes simulation

Dear Deva: I'm also trying working out how run gromacs on stampede with parallel. I just got some tests on 4.6 version and got similar speed as your single test. At least for 4.6 version, the parallel can be run by #SBATCH -N 1 #SBATCH -n 2 ibrun mdrun_mpi_gpu . I'm still making benchmark

[gmx-users] syntax for gmx distance

Dear all, I understand that this is quite a basic question, but I think I need a fresh set of eyes to figure out what¹s going on with gmx distance -select syntax. In my index file, I have 23 groups, two of which are ³ZINC² and ³CARBONYL² Based on numerous mail archive suggestions and the

[gmx-users] grompp error

Dear GROMACS users, I need to simulate a hyper branched polymer (a polyamidoamine dendrimer). I used the GROMOS53A6 to perform the simulation. But, I have a problem with defining the angles and dihedrals that are between two residues (because of dendrimers hyper branched structure). I can perform

[gmx-users] amber99bsc0 force field

Dear all Is there amber99bsc0 in gromacs default force fields? Best, Andrew -- 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

Re: [gmx-users] hi

Please use a descriptive subject line to draw attention to your specific problem and avoid spam filters. On 9/13/15 11:35 PM, Idriz Seferi wrote: Hi all, I have a question regarding Umbrella Sampling in gromacs 5.1. I am following the tutorial of Dr. Lemkul () and I am getting errors about