[gmx-users] Re: System has non-zero total charge: 2.570000e+00

> before energy minimization step , I performed the preprosessing step using > grompp  . However, there’s a note that : System has non-zero total charge: > 2.57e+00 “. > why the total charge of system is not an integer? The charge is too big to be the result of rounding. The first question i

Re: [gmx-users] System has non-zero total charge: 2.570000e+00

Itamar Kass wrote: Hi, If you have non water molecule in the box (eg protein) their charge might differ from 0. SO you might add ions in order to neutralize it. In general, that is a correct solution. But in the case of a +2.57 net charge, something is certainly wrong with the specie

Re: [gmx-users] System has non-zero total charge: 2.570000e+00

Justin A. Lemkul wrote: najwa drici wrote: hello Gromacs users, I have some problems about the total charge of system using Gromacs. I wanted to perform molecular dynamic simulation in box of SPC water. before energy minimization step , I performed the preprosessing step using grompp . How

Re: [gmx-users] help with periodic boundary conditions

Jarol E. Molina wrote: Hi all I am simulating a polymer chain and I need some help. At some simulation time, the polymer chain is outside the simulation box. I know that the option “pbc = xyz” into file grom.mdp is sufficient to have periodic boundary conditions. Can you help me The

[gmx-users] help with periodic boundary conditions

Hi all I am simulating a polymer chain and I need some help. At some simulation time, the polymer chain is outside the simulation box. I know that the option “pbc = xyz” into file grom.mdp is sufficient to have periodic boundary conditions. Can you help me Thanks -- Jarol

Re: [gmx-users] System has non-zero total charge: 2.570000e+00

najwa drici wrote: hello Gromacs users, I have some problems about the total charge of system using Gromacs. I wanted to perform molecular dynamic simulation in box of SPC water. before energy minimization step , I performed the preprosessing step using grompp . However, there’s a note tha

Re: [gmx-users] template.c

Chih-Ying Lin wrote: HI To use template.c 1. create a file to put template.c and Makefile.x86_64-unknown-linux-gnu together 2. under C compiler => type the command => make -f Makefile.x86_64-unknown-linux-gnu => type the command => cc -O -o template template.c -lm => type the comman

[gmx-users] System has non-zero total charge: 2.570000e+00

hello Gromacs users, I have some problems about the total charge of system using Gromacs. I wanted to perform molecular dynamic simulation in box of SPC water. before energy minimization step , I performed the preprosessing step using grompp . However, there’s a note that : System has non-z

[gmx-users] template.c

HI To use template.c 1. create a file to put template.c and Makefile.x86_64-unknown-linux-gnu together 2. under C compiler => type the command => make -f Makefile.x86_64-unknown-linux-gnu => type the command => cc -O -o template template.c -lm => type the command => ./template < template.i

Re: [gmx-users] Energy mimimization in AcOH box

Aditi Borkar wrote: Thanx Justin. I had tried that too. Using both parameters I get the same outcome. I notice that increasing the emtol to 2000 (that effectively reduces the number of steps my system undergoes before converging) retains most of the structure. Should I change the dielectric co

Re: [gmx-users] Energy mimimization in AcOH box

Thanx Justin. I had tried that too. Using both parameters I get the same outcome. I notice that increasing the emtol to 2000 (that effectively reduces the number of steps my system undergoes before converging) retains most of the structure. Should I change the dielectric constant of the solvent be

Re: [gmx-users] Energy mimimization in AcOH box

Aditi Borkar wrote: Dear All, Hello! I am simulating a protein in a box of 9M acetic acid. I have obtained the coordinates and gromacs topology for AcOH from PRODRG. The AcOH has net -1 charge and the topology file is as follows: PRODRG topologies generally produce unsatisfactory charges.

Re: [gmx-users] System has non-zero total charge: 1.999878e+00

zakiya wrote: > Hi Gromacs users, > I have some problems about the total charge of system using Gromacs. > I wanted to perform a protein denaturation simulation induced by urea. At > first, I added urea molecules into the box including one CI2 protein. Then I > performed the energy minimization s

Re: [gmx-users] problems running REMD on grids

Did you try to remove the "_" from your file name? On Sep 11, 2009, at 14:04, Anna Marabotti wrote: Dear gmx-users, I’m trying to perform some REMD calculations with GROMACS 4.0.5, and I found on the Wiki site these instructions: http://oldwiki.gromacs.org/index.php/REMD that I’m tryin

[gmx-users] System has non-zero total charge: 1.999878e+00

Hi Gromacs users, I have some problems about the total charge of system using Gromacs. I wanted to perform a protein denaturation simulation induced by urea. At first, I added urea molecules into the box including one CI2 protein. Then I performed the energy minimization step. However, there’s a

[gmx-users] Energy mimimization in AcOH box

Dear All, Hello! I am simulating a protein in a box of 9M acetic acid. I have obtained the coordinates and gromacs topology for AcOH from PRODRG. The AcOH has net -1 charge and the topology file is as follows: [ moleculetype ] ; Name nrexcl ACA 3 [ atoms ] ; nr type resnr resid at