[gmx-users] trjconv and g_clustsize

2011-12-26 Thread mohammad agha
Dear Prof. I have several questions about trjconv, please help me. In my simulation is created 2 micelles. 1- When I do 3 steps of micelle clustering as follows:   a- trjconv -f md.xtc -o a_cluster.gro-e 60 -pbc cluster  b- grompp -f md.mdp -c a_cluster.gro -o a_cluster.tpr  c- trjconv -f

[gmx-users] No default Angle types and Improper Dih. types

2011-12-26 Thread Lara Bunte
Hello after use of grompp I got the following errors: ERROR 1 [file topol.top, line 172]:   No default Angle types this error repeats ERROR 38 [file topol.top, line 233]:   No default Improper Dih. types this error repeats also Excluding 3 bonded neighbours molecule type 'Isoalloxazin'

[gmx-users] average pressure using g_energy

2011-12-26 Thread Efrat Exlrod
Hi, We have run an NPT equilibration on a protein embedded in a membrane and calculated the average pressure using g_energy. We then imported the resulting xvg file into excel and recalculated the average. The 2 numbers differed. Specifically, the gromacs average pressure was 0.942858 while

Re: [gmx-users] average pressure using g_energy

2011-12-26 Thread Mark Abraham
On 12/26/2011 10:43 PM, Efrat Exlrod wrote: Hi, We have run an NPT equilibration on a protein embedded in a membrane and calculated the average pressure using g_energy. We then imported the resulting xvg file into excel and recalculated the average. The 2 numbers differed. Specifically, the

Re: [gmx-users] No default Angle types and Improper Dih. types

2011-12-26 Thread Mark Abraham
On 12/26/2011 8:22 PM, Lara Bunte wrote: Hello after use of grompp I got the following errors: ERROR 1 [file topol.top, line 172]: No default Angle types grompp needs either parameters for the angle interaction on the line it is defined, or one able to be looked up from the [angletypes]

Re: [gmx-users] trjconv and g_clustsize

2011-12-26 Thread Mark Abraham
On 12/26/2011 7:53 PM, mohammad agha wrote: Dear Prof. I have several questions about trjconv, please help me. In my simulation is created 2 micelles. 1- When I do 3 steps of micelle clustering as follows: a- |trjconv -f md.xtc -o a_cluster.gro-e 60 -pbc cluster| | b- ||grompp -f md.mdp

[gmx-users] Problem with umbrella sampling and g_wham

2011-12-26 Thread Eric LeGresley
Hello all, For some time now I have been unable to find a solution to my problem. I am attempting to do umbrella sampling on a protein ligand system. To generate the starting configurations, I use the following mdp file: title = Protein-ligand complex MD Simulation define =

Re: [gmx-users] Problem with umbrella sampling and g_wham

2011-12-26 Thread Justin A. Lemkul
Eric LeGresley wrote: Hello all, For some time now I have been unable to find a solution to my problem. I am attempting to do umbrella sampling on a protein ligand system. To generate the starting configurations, I use the following mdp file: title = Protein-ligand complex MD

Re: [gmx-users] how to use gromacs 4.5.5's temple?

2011-12-26 Thread Mark Abraham
On 12/25/2011 9:44 PM, ?? wrote: Dear teacher, how to use gromacs 4.5.5's temple? I expect that it is not meant to be functional. It's meant to be a template from which you can write functional code without having to work too hard on making it work like GROMACS tools work. Mark i make

Re: [gmx-users] oligosaccharide oplsaa .itp

2011-12-26 Thread Mark Abraham
On 12/25/2011 7:56 PM, Ashalatha Sreshty wrote: Dear All, I have a problem running gromacs for a oligosaccharide. it has 14 units sugars containing glucose, mannose and N-acetyl glucosamine units. I want to do MD simulations for this with opls aa force field. For this I have generated the .itp

[gmx-users] (no subject)

2011-12-26 Thread Nidhi Katyal
Dear all, I am trying to create tmao box.Energy minimization, simulated annealing (Cooling under high pressure and again heating at normal pressure) as well as final equilibration ran smoothly. But finally I got a box where all water molecules got accumulated in two three small region within the