[gmx-users] pdo files in umbrella sampling

2012-02-18 Thread abbas yousefpour
Dear gmx users Could you please help me to create pdo files?I have finished my umbrella sampling with position but g_wham wants pdo files but I can not find any option to have these files after my run or create them.I dont know what to do.Thanks a lot -- gmx-users mailing listgmx-users@gromac

Re: [gmx-users] Free energy between surfaces

2012-02-18 Thread Steven Neumann
Cheers pal! :) Steven On Sat, Feb 18, 2012 at 9:42 AM, Jianguo Li wrote: > One way to get the free energy is to measure the force as a function of > distance and do the integration to get the PMF, as used in the paper: > Ronen Zangi, Morten Hagen, and B. J. Berne. 2007. Effect of Ions on the >

[gmx-users] xy option in g_rdf

2012-02-18 Thread Andrew DeYoung
Hi, If you have time, I have a question about the -xy option in g_rdf. I'm a little afraid that this may be silly question and the answer might be obvious in hindsight, but I have been having difficulty finding the answer. Thanks. As we all know, g_rdf computes radial distribution functions of,

Re: [gmx-users] Shift function: rcoulomb-switch

2012-02-18 Thread Juliette N.
Sorry I meant he default rcoulomb-switch is 0. I am using OPLSAA. Just confused 0.1 nm switch distance to rc=1.1 doesnt give artifact. I think i am confusing this with the buffer zone needed between rc and rlist! On 18 February 2012 10:21, Mark Abraham wrote: > On 19/02/2012 2:01 AM, Juliette

Re: [gmx-users] Shift function: rcoulomb-switch

2012-02-18 Thread Mark Abraham
On 19/02/2012 2:01 AM, Juliette N. wrote: Hi, I am trying to figure out the best setting for cut offs and r_switch for my system based on shift functions. coulombtype = Shift vdw-type= Shift rcoulomb-switch = 1 rvdw-switch = 1 ; Cut-offs

[gmx-users] Shift function: rcoulomb-switch

2012-02-18 Thread Juliette N.
Hi, I am trying to figure out the best setting for cut offs and r_switch for my system based on shift functions. coulombtype = Shift vdw-type= Shift rcoulomb-switch = 1 rvdw-switch = 1 ; Cut-offs rlist = 1.35 rcoulomb

Re: [gmx-users] g_analyze -ee

2012-02-18 Thread Justin A. Lemkul
dina dusti wrote: Dear Gromacs Specialists, Sometimes, when I do "g_analyze -f .xvg -av -ee error.xvg" , I take following warning, and I don't know how to fix it. Set 1: err.est. 0.000596502 a 0.29217 tau1 24.8856 tau2 443.641 Warning: tau2 is longer than the length of the data (

Re: [gmx-users] Umbrella_pull_simulation

2012-02-18 Thread Justin A. Lemkul
shahid nayeem wrote: Dear All I am doing umbrella sampling for a protein complex. After analysis I am finding that prifle.xvg has not converged. Now I want to extend simulation. I have already pulled one chain to the length of the box. Can I further pull by extending the box size and add mo

Re: [gmx-users] The promblem of force field

2012-02-18 Thread Mark Abraham
On 18/02/2012 7:50 PM, xiaojiong wrote: Dear, My receptor is membrane proteins,then I get protein-ligand complex.I want to do MD simulations in DPPC.I use the GROMOS96 53a6 force field modified in order to include Berger’s parameters for lipids .The topology for the ligand was created employin

Re: [gmx-users] a question about force fields

2012-02-18 Thread Mark Abraham
On 18/02/2012 7:23 PM, Banafsheh Mehrazma wrote: Dear all; I am wondering if the amber99 in gromacs package is the same as PARM99 in Amber package, so that I can use the new modified parameters (which is made in Amber package) in my simulation in gromacs? Or should I make some changes? These sh

[gmx-users] g_analyze -ee

2012-02-18 Thread dina dusti
Dear Gromacs Specialists, Sometimes, when I do "g_analyze -f  .xvg -av -ee error.xvg" , I take following warning, and I don't know how to fix it. Set   1:  err.est. 0.000596502  a 0.29217  tau1 24.8856  tau2 443.641 Warning: tau2 is longer than the length of the data (864000) the st

Re: [gmx-users] Free energy between surfaces

2012-02-18 Thread Jianguo Li
One way to get the free energy is to measure the force as a function of distance and do the integration to get the PMF, as used in the paper: Ronen Zangi, Morten Hagen, and B. J. Berne. 2007. Effect of Ions on the Hydrophobic Interaction betweenTwo Plates. J. AM. CHEM. SOC. 2007, 129, 4678-468

[gmx-users] Free energy between surfaces

2012-02-18 Thread Steven Neumann
Dear Gmx Users, I am wondering whether you know a technique for calculating the free energy between charged surfaces - I want to calculate distance when the deltaG=0 so that the surfaces are in equilibrium - closer distance will make that they repeal each other, longer (deltaG<0). Will Umbrella Sa

[gmx-users] The promblem of force field

2012-02-18 Thread xiaojiong
Dear, My receptor is membrane proteins,then I get protein-ligand complex.I want to do MD simulations in DPPC.I use the GROMOS96 53a6 force field modified in order to include Berger’s parameters for lipids .The topology for the ligand was created employing the server PRODRG 2.5 Beta. When I f

[gmx-users] a question about force fields

2012-02-18 Thread Banafsheh Mehrazma
Dear all; I am wondering if the amber99 in gromacs package is the same as PARM99 in Amber package, so that I can use the new modified parameters (which is made in Amber package) in my simulation in gromacs? Or should I make some changes? Best regards; Banafsheh -- gmx-users mailing listgmx-us