Re: [gmx-users] Problem in implementing do_dssp

Maybe you could first try chmod +x dssp-2.0.4-linux-i386 , and then do_dssp. On Thursday, 7 April 2016, 13:45, Rishikesh Parulekar wrote: Hi justin Lemkul dssp binary from usr/local/bin is working fine on its own but the command it is showing for secondary structure determination is di

Re: [gmx-users] How to scale epsilon parameters of Lennard-Jones term in .top file?

To run REST in gmx using lamda-dynamics, you need to edit both ffnonbonded.itp and ffbonded.itp. In ffnonbonded.itp, you need to define a new atom type corresponding to state B, you need to add something like:; name             bond_type       mass          charge   ptype  sigma  ep

Re: [gmx-users] Errors about dihidral angle type 9 in free energy perturbation

other way to make it work? Cheers,Jianguo On Thursday, 4 December 2014, 20:55, Justin Lemkul wrote: On 12/4/14 2:32 AM, Jianguo Li wrote: > Dear All, > I am trying to use free energy perturbation module of gromacs to do > hamiltonian replica exchange using CHARMM27 all-a

[gmx-users] Errors about dihidral angle type 9 in free energy perturbation

Dear All, I am trying to use free energy perturbation module of gromacs to do hamiltonian replica exchange using CHARMM27 all-atom force field (with CMAP) - version 2.0 I am using 4.5.4 version of gromacs according to manual (Table 5.5), it allows to perturb dihedral angles: proper dih. multi, 

[gmx-users] GB parameters for DNA

Dear everyone, I would like to simulate a DNA-protein complex using implicit solvent model. Anyone has the GB parameters for phosphorus atom?  I searched the mailing list, but did not find the answer. Thanks in advance Cheers, Jianguo -- Gromacs Users mailing list * Please search the archiv

Re: [gmx-users] Hydrogen bond with chlorine

Hi Dhawal, One way you can try is to manually change ｔｈｅ name of chloride to oxygen so that the g_hbond code can treat the new atom name as acceptors. Just modify .gro file, .top file and ions.itp file and get a new tpr file. And use the rerun option of mdrun to get a new trajectory.  Then you

[gmx-users] GTX card vs Kepler card

Dear All, I have an doubt on the GPU hardware. Recently I heard from a nvidia person that unlike Kepler card, GTX card does not have the memory check and correction. It is no problem for gaming, but may lead to wrong results for scientific computing. I am just wondering how this will affect t

Re: [gmx-users] pressure based replica exchange

yet. > > > > The exchange criteria is always of the form min(1,exp(-X), where X = > > \beta(Delta (beta U) + Delta (beta P V)).  Where P, beta, and U can > > vary with state. > > > > What is in is temperature replica exchange with NPT, where beta > > changes, bu

Re: [gmx-users] pressure based replica exchange

with NPT, where beta changes, but P stays the same. On Thu, Dec 12, 2013 at 1:40 AM, Jianguo Li wrote: > Thanks very much. As you suggested, making T with small increments such as > 300.0, 300.0001, 300.0002 ... leads to complaints :-) > > I am trying to do replica exchange at d

Re: [gmx-users] pressure based replica exchange

pressure+temperature+Hamiltonian replica exchange has been implemented in Gromacs. If yes, what is the general equation of acceptance criteria? Cheers, Jianguo On Tuesday, 10 December 2013, 17:49, Mark Abraham wrote: On Tue, Dec 10, 2013 at 1:47 PM, Jianguo Li wrote: Dear All, >

[gmx-users] pressure based replica exchange

Dear All, Is it possible to do pressure based replica exchange simulations in gromacs? Basically I want to do replica exchange simulations for my membrane system at different surface tensions. If I just set different pressures in the mpd file, then the mdrun will complain "systems are all the s