Re: [gmx-users] gold-protein simulation

2013-01-05 Thread Justin Lemkul
On 1/5/13 2:54 PM, fatemeh ramezani wrote: HI I'm simulating gold nanoparticle interaction with protein by oplsaa forcefield . I added AU-AU Lennard Jones parameters to ffnonbonded.itp and also I added what was necessary for AU atom simulation in .atp , .rtp files. what I see After simula

Re: [gmx-users] gold-protein simulation stop by error in equilibrum step

2012-12-06 Thread Martin Hoefling
Am 06.12.2012 21:16, schrieb Justin Lemkul: > > > On 12/6/12 3:12 PM, fatemeh ramezani wrote: >> hello >> I want to simulate gold nanoparticles with proteins. I've made ​​a >> PDF file containing the nanoparticles and proteins, using Hayprkm >> software.then Ihave used thisPDF fileto start the simu

Re: [gmx-users] gold-protein simulation stop by error in equilibrum step

2012-12-06 Thread Justin Lemkul
On 12/6/12 3:12 PM, fatemeh ramezani wrote: hello I want to simulate gold nanoparticles with proteins. I've made ​​a PDF file containing the nanoparticles and proteins, using Hayprkm software.then Ihave used thisPDF fileto start the simulation by gromacs. But in the early stage of equilibriu

[gmx-users] gold-protein simulation stop by error in equilibrum step

2012-12-06 Thread fatemeh ramezani
hello I want to simulate gold nanoparticles with proteins. I've made ​​a PDF file containing the nanoparticles and proteins, using Hayprkm software.then Ihave used thisPDF fileto start the simulation by gromacs. But in the early stage of equilibrium, I am faced with the following error. applica