Re: [gmx-users] coenzyme-protein complex

2014-02-02 Thread Mostafa Javaheri
Dear Justin My final .xtc rmsd graph starts about 4 nm and after some steps it falls down to 0.3 and quickly goes up again, totally it is tossing around a straight line near 4 nm, what did I do wrong? As mentioned in my previous mail about centering of protein inside the box, the gro file was

[gmx-users] pbc problem

2014-02-02 Thread Atila Petrosian
Dear Justin and Tsjerk you said Some tools handle PBC properly, some don't . I want to know exactly which tools of gromacs handle PBC properly. Can I find these tools in manual? I did simulation of a system containing protein and cnt using gromacs 4.5.6. When I see trajectory by VMD, in some

Re: [gmx-users] pbc problem

2014-02-02 Thread Justin Lemkul
On 2/2/14, 7:15 AM, Atila Petrosian wrote: Dear Justin and Tsjerk you said Some tools handle PBC properly, some don't . I want to know exactly which tools of gromacs handle PBC properly. Can I find these tools in manual? No, because it's not possible to test every single command that

[gmx-users] Bond interaction exclusions

2014-02-02 Thread Xu Dong Huang
Dear all, I am unclear about the bond exclusion properties within gromacs. Using a martini model system, what is the default behavior of setting [moleculetype] ;name exclusions eth 1 exclusions to 1? How do I find out what kind of interaction it is excluding? I am interested in finding

Re: [gmx-users] Bond interaction exclusions

2014-02-02 Thread Justin Lemkul
On 2/2/14, 11:29 AM, Xu Dong Huang wrote: Dear all, I am unclear about the bond exclusion properties within gromacs. Using a martini model system, what is the default behavior of setting [moleculetype] ;name exclusions eth 1 exclusions to 1? How do I find out what kind of interaction

Re: [gmx-users] Bond interaction exclusions

2014-02-02 Thread XAvier Periole
Hi, The first line eth1 tells it all. In that molecule all non-bonded interactions between first bonded neighbors will be excluded. Thus the 1-3, 1-4 (and so on) non-bonded interactions will be included. You may add additional exclusions in the [ exclusion ] section of your topology.

Re: [gmx-users] codes for non-bonded function selection (NBF)

2014-02-02 Thread Mark Abraham
Hi, As you can see in the comment at the top of that file, you will need to make matching changes to some arrays in src/gmxlib/names.c Mark On Sat, Feb 1, 2014 at 3:11 AM, Makoto Yoneya makoto-yon...@aist.go.jpwrote: Dear Gromacs exparts: I'd like to add the non-boded function selection

Re: [gmx-users] Bond interaction exclusions

2014-02-02 Thread Mark Abraham
On Sun, Feb 2, 2014 at 5:29 PM, Xu Dong Huang xudonghm...@gmail.com wrote: Dear all, I am unclear about the bond exclusion properties within gromacs. Using a martini model system, what is the default behavior of setting [moleculetype] ;name exclusions eth 1 exclusions to 1? The

Re: [gmx-users] simulating multiple molecules in a box

2014-02-02 Thread Mark Abraham
On Sun, Feb 2, 2014 at 8:28 PM, ibrahim khalil ibrahim.khalil.c...@gmail.com wrote: hi, i am new to gromacs. i was trying simulate multiple (eg. 3 or 4 ) carbon nanotubes in a single box. The way I am trying to do is ... 1. Take both pdb files, merge them(using pymol) according to my

Re: [gmx-users] Simulating spherocylinders

2014-02-02 Thread Mark Abraham
No. Mark On Sun, Feb 2, 2014 at 7:25 PM, Sanku M msank...@yahoo.com wrote: Dear Gromacs users Is it possible to simulate md of rigid spherocylinders in grimaces? Thanks Sanku -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Replica Exchange MD

2014-02-02 Thread bharat gupta
Dear GMX Users, I am trying to apply the REMD to study the difference between the folding free energy of a 24 residue peptide with two different conformations. As I am short of required number of processors for REMD in explicit water, I am trying my luck with implicit solvent. I have come across