[gmx-users] Non-zero total charge

2011-09-01 Thread Munishika Kalia
Hi, My system had a no zero total charge: System has non-zero total charge: 6.30e+01 I used genion to neutralize the system by adding 6 CL ions. After updating the topology file, the system still seems to have the same problem. It still has a non-zero total charge: System has non-zero

Re: [gmx-users] Non-zero total charge

2011-09-01 Thread Justin A. Lemkul
Munishika Kalia wrote: Hi, My system had a no zero total charge: System has non-zero total charge: 6.30e+01 I used genion to neutralize the system by adding 6 CL ions. After updating the topology file, the system still seems to have the same problem. It still has a non-zero total

[gmx-users] Non-zero total charge

2011-09-01 Thread chris . neale
6.30e+01 = 63 -- original message -- My system had a no zero total charge: System has non-zero total charge: 6.30e+01 I used genion to neutralize the system by adding 6 CL ions. After updating the topology file, the system still seems to have the same problem. It still has a

[gmx-users] Non zero total charge

2011-09-01 Thread Munishika Kalia
Hi, The genion command i used is genion -s genion.tpr -o ago_water_ions.gro -nn 6 I used this to add 6 CL ions and i got the following error:   System has non-zero total charge: 5.70e+01 So i should add another 5 CL ions to neutralize the system? Many thanks, Munishika -- gmx-users

Re: [gmx-users] Non zero total charge

2011-09-01 Thread Matthew Zwier
Not 5. 57. Look at the exponent. On Thu, Sep 1, 2011 at 11:46 AM, Munishika Kalia munishikaka...@yahoo.com wrote: Hi, The genion command i used is genion -s genion.tpr -o ago_water_ions.gro -nn 6 I used this to add 6 CL ions and i got the following error:   System has non-zero total

Re: [gmx-users] Non zero total charge

2011-09-01 Thread Andrew Paluch
I believe your problem is that you do not understand scientific notation. 5.70e+01 = 57. Cl- has a charge of -1. Need I say more. On Thu, Sep 1, 2011 at 11:46 AM, Munishika Kalia munishikaka...@yahoo.comwrote: Hi, The genion command i used is genion -s genion.tpr -o ago_water_ions.gro

Re: [gmx-users] non-zero total charge for water

2007-12-13 Thread Mark Abraham
JMandumpal wrote: It says, System has non-zero total charge: -2.58e-01. [ molecules ] SOL 258 There's a pattern here. tip5P.itp file --- [ moleculetype ] ; molname nrexcl SOL2

[gmx-users] non-zero total charge for water

2007-12-13 Thread JMandumpal
Dear Gromacs users, I built .tpr file prior to energy minimisation of box of tip5p water molecule. I received the output like this: calling /lib/cpp... processing topology... Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated