Re: [gmx-users] Doubt regarding nrexcl parameter in topology

Dear Bipin, With nrexcl = 3 it excludes neighbours 3 bonds away, in this case your (ii) option falls. But an extra LJ and electrostatic interactions, is added between 1-4 pairs, if gen-pair is yes for the force field. These interactions are scaled by their respective fudge factor. For gromos ff, t

[gmx-users] Doubt regarding nrexcl parameter in topology

Dear All, I have a doubt regarding the definition of nrexcl parameter in topology of a molecule (Gromos force field) As mebtioned in the Gromacs manual, nrexcl = 3 stands for excluding non-bonded interactions between atoms that are no further than 3 bonds away, so does it mean that: (i) Exclud

Re: [gmx-users] TIP4P equilibration

Hi, What does the diff tool tell you about the number of water molecules you have in each case, and the contents of your .mdp file in each case? Mark On Fri, Jan 16, 2015 at 10:19 PM, Aranha, Michelle wrote: > Hi, > > I have a box of water 6nm * 6nm * 14nm, minimized and subsequently > equili

[gmx-users] TIP4P equilibration

Hi, I have a box of water 6nm * 6nm * 14nm, minimized and subsequently equilibrated in NVT. After NVT equilibration when I equilibrate in NPT using Berendsen Barostat to 1 bar and 300 K trying different Tau-P values, the system's volume keeps increasing and the density of the system rapidly d

Re: [gmx-users] fe2s2 simulation

Hi Somlata, For GROMACS to recognize your FES moiety you will have to determine the force field parameters for the forcefield which you want to use and then update the GROMACS databases. Without GOMACS having the necessary parameters for the atoms in your FES moiety in its forcefield database you

[gmx-users] fe2s2 simulation

Hello all, I want to carry out MD simulation on a protein containing iron-sulfur clusters(Fe2S2) using Gromacs. I have used CHARMM and AMBER force field. But every time I get the error "The residue topology parameter for FES is not found". But I found in literature that this type of complexes are

[gmx-users] AMBER99 topology for ADP

Hello all, I want to carry out MD simulation on a protein containing iron-sulfur clusters(Fe2S2) using Gromacs. I have used CHARMM and AMBER force field. But every time I get the error "The residue topology parameter for FES is not found". But I found in literature that this type of complexes are

[gmx-users] dipole derivative

Dear all, Has anyone calculated the dipole derivative with respect to normal mode coordinates in gromacs? It shoule be something like one of the outputs from DIPOles command in CHARMM software. Thanks, Yao -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.or

Re: [gmx-users] potential energy

Hi Justin, I haven't come to a conclusion yet and need your help! I attached a copy of a typical g_energy -f ener.edr -o copied from terminal and an .mdp file. Bond18506.5 501625.68 -301.714 (kJ/mol) Angle 9839.32 13580.506

Re: [gmx-users] Cluster recommendations

Hi David, On 16 Jan 2015, at 12:28, David McGiven wrote: > Hi Carsten, > > Thanks for your answer. > > 2015-01-16 11:11 GMT+01:00 Carsten Kutzner : > >> Hi David, >> >> we are just finishing an evaluation to find out which is the optimal >> hardware for Gromacs setups. One of the input syste

Re: [gmx-users] Cluster recommendations

Hi Carsten, Thanks for your answer. 2015-01-16 11:11 GMT+01:00 Carsten Kutzner : > Hi David, > > we are just finishing an evaluation to find out which is the optimal > hardware for Gromacs setups. One of the input systems is an 80,000 atom > membrane channel system and thus nearly exactly what y

Re: [gmx-users] Cluster recommendations

Hi David, we are just finishing an evaluation to find out which is the optimal hardware for Gromacs setups. One of the input systems is an 80,000 atom membrane channel system and thus nearly exactly what you want to compute. The biggest benefit you will get by adding one or two consumer-class GPU

Re: [gmx-users] Debugging 'inconsistent shifts'

On 15 January 2015 at 19:44, Justin Lemkul wrote: > > > On 1/15/15 11:25 AM, Kalev Takkis wrote: > >> On 15 January 2015 at 00:09, Justin Lemkul wrote: >> >> >>> >>> On 1/14/15 4:44 PM, Kalev Takkis wrote: >>> >>> Hi, list! GROMACS complains about inconsistent shifts and suggests me t

Re: [gmx-users] Using -all flag in g_angle command

Got it! Thank you. Hi, > > Did you look at the full contents of the output files? I expect they're in > the same file produced without -all. > > Mark > > On Thu, Jan 15, 2015 at 12:47 PM, GAYATHRI S > wrote: > >> The following command generated only two outputs - angaver.xvg and >> angdist.xvg:

Re: [gmx-users] Atomtype P,SI not found from grompp

Dear Justin, Many thanks. It's clear to me now. I will contact them for this issue. Regards, Jennifer On Thu, Jan 15, 2015 at 10:43 PM, Justin Lemkul wrote: > > > On 1/15/15 1:58 PM, Jennifer Vo wrote: > >> Dear Justin, >> Thanks again! I have downloaded the topology from Automated Topology >> B