RE: [gmx-users] error with indexfile

2013-01-04 Thread Awasthi, Neha
First check your .gro file and your .top file, to make sure atom 6518 (or Water) is consistently defined. Next step would be to make sure this atom features in the index file within a "correct group". In some cases, if a single atom is left out and not part of any group in the index file, it gives

Re: [gmx-users] Re: Simulation of 2D lattice model

2013-01-04 Thread James Starlight
Justin, thanks again for explanation. I've tried examine that parameters more carefully. E.g in my system with 2 atom types I defined in topology [ atomtypes ] ;name at.num mass charge ptype c6 c12 CH26 0.000 0.000 A 0.0023406244 4.937284e-06 ; CB

Re: [gmx-users] error with indexfile

2013-01-04 Thread Kieu Thu Nguyen
Thank Neha ! I follow your advices but this error still appear. I don't know why. By the way, does anybody know why there are not ions in topology file in Martini CG-MD. Because I see the system has not zero charge, i don't understand why the CG system not be neutralized by ions. Thanks and regar

[gmx-users] Reducing trr storage volume

2013-01-04 Thread Shima Arasteh
Dear users, I'm simulating a system of protein/water/popc/ions. The peptide is inserted through the transmembrane, and the peptide acts as a channel. In order to reduce the trajectory storage volume, I need to use xtc-grps in .mdp file. In my system, I'd rather to store the positions of peptide,

Re: [gmx-users] error with indexfile

2013-01-04 Thread Justin Lemkul
On 1/4/13 12:51 AM, Kieu Thu Nguyen wrote: Dear All, When using the command grompp -f equi.mdp -c membedded.gro -p merged.top -n index.ndx -o equilibrate.tpr The error is Fatal error: Invalid atom number 6518 in indexfile How can i fix this ? Hard to say. You haven't told us what's in the s

Re: [gmx-users] error with indexfile

2013-01-04 Thread Justin Lemkul
On 1/4/13 5:06 AM, Kieu Thu Nguyen wrote: Thank Neha ! I follow your advices but this error still appear. I don't know why. You'll have to show us exactly what you're doing to get any solid advice. Consider what I posted earlier. Usually the mismatch occurs because you are using a coordin

Re: [gmx-users] Re: Simulation of 2D lattice model

2013-01-04 Thread Justin Lemkul
On 1/4/13 5:01 AM, James Starlight wrote: Justin, thanks again for explanation. I've tried examine that parameters more carefully. E.g in my system with 2 atom types I defined in topology [ atomtypes ] ;name at.num mass charge ptype c6 c12 CH26 0.000

Re: [gmx-users] Charmm units in Gmx

2013-01-04 Thread Justin Lemkul
On 1/4/13 9:16 AM, Steven Neumann wrote: Dear All, What are the units used in Charmm ff in Gromacs for nonbonded parameters? Is that kJ/mol for Epsilon or kcal/mol ? Is that A or nm for sigma? See the manual, chapter 2. Particularly Tables 2.1 and 2.2. -Justin --

Re: [gmx-users] Reducing trr storage volume

2013-01-04 Thread Justin Lemkul
On 1/4/13 11:09 AM, Shima Arasteh wrote: Dear users, I'm simulating a system of protein/water/popc/ions. The peptide is inserted through the transmembrane, and the peptide acts as a channel. In order to reduce the trajectory storage volume, I need to use xtc-grps in .mdp file. In my system,

Re: [gmx-users] Re: Simulation of 2D lattice model

2013-01-04 Thread James Starlight
Justin, thanks for explanation again! So if I understood correctly in the ffnonbonded c6 correspond to the attraction term and c12 to the repulsion term doestn't it ? So might the vdw radius of the atom be increased/ deacreased via corrections in the c6 term ? mass charge ptype