[gmx-users] (no subject)

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[gmx-users] Obtain the flux of water

Dear all,  Whether there is a program in Gromacs that would directly or indirectly obtained the flux of water ? How to obtain the flux water in Gromacs ?  Best Regards  -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the a

[gmx-users] Method insert ion

If I do not use for insert ions into the water from genion and Ions put in the file pdb whether Gromacs no problem with it ? Whether the behavior of ions such as ions that enter via genion ? 4.pdb : ATOM      1  CL   CL   145      23.580  24.000  -0.020  1.00  0.00             ATOM      2  CL

[gmx-users] Applied electric field on the pure water

The simulation box contains just water molecules ** water.pdb ** ATOM     1   OW  SOL    1       19.350   2.371   0.000  0.00  0.00              ATOM     2   HW1 SOL    1       18.600   2.951   0.000  0.00  0.00              ATOM     3   HW2 SOL    1       20.100   2.951   0.000  0.00  0.00      

[gmx-users] Applied electric field on the pure water

The simulation box contains just water molecules ** water.pdb ** ATOM     1   OW  SOL    1       19.350   2.371   0.000  0.00  0.00              ATOM     2   HW1 SOL    1       18.600   2.951   0.000  0.00  0.00              ATOM     3   HW2 SOL    1       20.100   2.951   0.000  0.00  0.00      

[gmx-users] Applied electric field on the pure water

Dear users The simulation box contains just water molecules Commands pdb2gmx -f water.pdb -posrefc 0 Force Field : AMBER99SB-ILDN  - Water TIP3P editconf -f conf.gro -bt cubic -box 5 5 5 genbox -cp out.gro -cs spc216.gro -o 5.gro -p topol.top grompp -f min.mdp -c 5.gro -p topol.top mdrun

[gmx-users] Re: applied electric field on the pure water

Dear users The simulation box contains just water molecules Commands pdb2gmx -f water.pdb -posrefc 0 Force Field : AMBER99SB-ILDN  - Water TIP3P editconf -f conf.gro -bt cubic -box 5 5 5 genbox -cp out.gro -cs spc216.gro -o 5.gro -p topol.top grompp -f min.mdp -c 5.gro -p topol

[gmx-users] applied electric field on the pure water

Dear users The simulation box contains just water molecules Commands pdb2gmx -f water.pdb -posrefc 0 Force Field : AMBER99SB-ILDN  - Water TIP3P editconf -f conf.gro -bt cubic -box 5 5 5 genbox -cp out.gro -cs spc216.gro -o 5.gro -p topol.top grompp -f min.mdp -c 5.gro -p topol

[gmx-users] calculate potential in the box contain ions

Dear users The simulation box contains sodium and chloride ions start simulation pdb2gmx -f ion.pdb -posrefc 0 Force Field : AMBER99SB-ILDN  - Water TIP3P editconf -f conf.gro -bt cubic -box 3 3 3 genbox -cp out.gro -cs spc216.gro -o 5.gro -p topol.top grompp -f minim.mdp -c 5.gro -p topol

[gmx-users] calculate potential in the box contain ions

Deer users The simulation box contains sodium and chloride ions start simulation pdb2gmx -f ion.pdb -posrefc 0 Force Field : AMBER99SB-ILDN  - Water TIP3P editconf -f conf.gro -bt cubic -box 3 3 3 genbox -cp out.gro -cs spc216.gro -o 5.gro -p topol.top grompp -f minim.mdp -c 5.gro -p topo

[gmx-users] ignore H-bond

Deer users. I want to ignore the hydrogen bonds in water. My system consists of ions and water molecules. Is there any way ignore hydrogen bonding of water ? Regards saeed -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the arc

[gmx-users] Ion distribution around Cl fix

Dear All I want to simulate a  boxfilledwater that includes 10 sodium ion and 9 chloride ion . a chlorine fixed placein center of box simulation to see how it affects the distribution ions . Two graphs were obtained for the distribution of ions than to Cl fix (chlorine fixin center of box) Ques

[gmx-users] Re: Ion distribution around Cl fix

Dear All I want to simulate a  boxfilledwater that includes 10 sodium ion and 9 chloride ion . a chlorine fixed placein center of box simulation to see how it affects the distribution ions . Two graphs were obtained for the distribution of ions than to Cl fix (chlorine fixin center of box) Quest

[gmx-users] Ion distribution around Cl fix

- Forwarded Message - From: Saeid Akbarshahi To: "gmx-users@gromacs.org" Sent: Wednesday, July 6, 2011 10:44 PM Subject: Ion distribution around Cl fix Dear All Question : Problem : Distribution of sodium and chloride ions than chlorine fixed placein center of box si

[gmx-users] Ion distribution around Cl fix

Dear All Question : Problem : Distribution of sodium and chloride ions than chlorine fixed placein center of box simulation I wanted to ask which graphs the density of sodium is correct ? Box : 2.65 *2.65 *2.65 nm force field : AMBER99SB-ILDN Number of Na : 10 Number of Cl : 9 Number of Cl f

[gmx-users] Ion distribution around Cl fix

Dear All Problem : Distribution of sodium and chloride ions than chlorine fixed placein center of box simulation I wanted to ask which graphs the density of sodium is correct ? Box : 2.65 *2.65 *2.65 nm force field : AMBER99SB-ILDN Number of Na : 10 Number of Cl : 9 Number of Cl fix  : 1 Time :

[gmx-users] Register

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