Re: [gmx-users] Fw: The results of your email commands

2012-01-01 Thread Mark Abraham
On 1/01/2012 9:38 PM, banafsheh mehrazma wrote: Hi everyone, I am studying a paper about a DNA simulation using Gromacs and I encountered this in ion addition step: Na+ were added by replacing a solvent molecule at ca. 6 Å from the phosphorus in the direction of the bisector of the angle ?O1P-

Re: [gmx-users] grompp error for CNT+surfactant simulation

2012-01-01 Thread Justin A. Lemkul
niaz poorgholami wrote: Dear all I am using Gromacs 4.5.3 to simulate a system including: CNT+water+surfactant and I want to use opls force field for my whole system. so far I have done following things: 1.I copied oplsaa.ff folder in my working directory. 2.I added following lines to atomnam

Re: [gmx-users] After installation help

2012-01-01 Thread Willian Pereira Felix
Hey Mark, thanks for your help. It was extremely useful, now it's solved and running XD. Nice year friend :) Willian Felix On Sat, Dec 31, 2011 at 10:36 PM, Mark Abraham wrote: > On 31/12/2011 11:58 PM, Willian Pereira Felix wrote: > > Hello buddies, > > I'm a very beginner in gromacs and I j

[gmx-users] grompp error for CNT+surfactant simulation

2012-01-01 Thread niaz poorgholami
Dear all I am using Gromacs 4.5.3 to simulate a system including: CNT+water+surfactant and I want to use opls force field for my whole system. so far I have done following things: 1.I copied oplsaa.ff folder in my working directory. 2.I added following lines to atomname2type.n2t Copls_9950

Re: [gmx-users] Segmentation fault

2012-01-01 Thread Mark Abraham
On 2/01/2012 12:35 AM, Saba Ferdous wrote: Dear Gromacs Experts, I am having problem in execution of a command in Gromacs, thats when i use dssp for secondary structure analysis. it gives error: Reading file md_0_10.tpr, VERSION 4.5.5 (single precision) Reading file md_0_10.tpr, VERSION 4.5.

[gmx-users] Segmentation fault

2012-01-01 Thread Saba Ferdous
Dear Gromacs Experts, I am having problem in execution of a command in Gromacs, thats when i use dssp for secondary structure analysis. it gives error: Reading file md_0_10.tpr, VERSION 4.5.5 (single precision) Reading file md_0_10.tpr, VERSION 4.5.5 (single precision) Segmentation fault (core

[gmx-users] Fw: The results of your email commands

2012-01-01 Thread banafsheh mehrazma
Hi everyone,  I am studying a paper about a DNA simulation using Gromacs and  I encountered this in ion addition step: Na+ were added by replacing a solvent molecule at ca. 6 Å from the phosphorus in the direction of the bisector of the angle ∠O1P-P-O2P (O1P and O2P being the phosphate nonbridg

Re: [gmx-users] Charge fitting

2012-01-01 Thread David van der Spoel
On 2012-01-01 10:11, parto haghighi wrote: Dear GMX usesr, I have to do charge fitting for a small molecule like ethanol. I have applied PRODRG to generate .gro and .itp for ethanol but it has wrong atomic charge. To correct it I have to use gromos 43a1 force field parameters to assign charges o

[gmx-users] Charge fitting

2012-01-01 Thread parto haghighi
Dear GMX usesr, I have to do charge fitting for a small molecule like ethanol. I have applied PRODRG to generate .gro and .itp for ethanol but it has wrong atomic charge. To correct it I have to use gromos 43a1 force field parameters to assign charges on each atom (Is it right?) I have red a pape