Re: [gmx-users] Generate an Index File

2009-11-12 Thread Justin A. Lemkul
Jack Shultz wrote: I am trying to run g_dist c:\ProgramData\BOINC\slots\0>g_dist.exe -f md.xtc -s md.tpr --- Program g_dist, VERSION 4.0.5 Source code file: futil.c, line: 330 File input/output error: index.ndx --

Re: [gmx-users] Generate an Index File

2009-11-12 Thread Mark Abraham
Jack Shultz wrote: I am trying to run g_dist c:\ProgramData\BOINC\slots\0>g_dist.exe -f md.xtc -s md.tpr --- Program g_dist, VERSION 4.0.5 Source code file: futil.c, line: 330 File input/output error: index.ndx

[gmx-users] Generate an Index File

2009-11-12 Thread Jack Shultz
I am trying to run g_dist c:\ProgramData\BOINC\slots\0>g_dist.exe -f md.xtc -s md.tpr --- Program g_dist, VERSION 4.0.5 Source code file: futil.c, line: 330 File input/output error: index.ndx -

Re: [gmx-users] Adsorption energy of a single molecule

2009-11-12 Thread Mark Abraham
Darrell Koskinen wrote: Hi Mark, No, I am not trying to build a random number generator and hope that I am not moving in this direction : ) My definition of adsorption energy would be the difference in energy when two species are at an infinite distance and the energy when these species are

Re: [gmx-users] Density histogram in Ramachandran plot

2009-11-12 Thread Mark Abraham
ms wrote: Hi, I wonder if there is an easy way I am missing to get a density histogram from the Ramachandran plot over a trajectory as outputted by g_rama. All I see are big, uniform black blobs and they're not helpful, because with tons of data points a density plot would be much more informati

[gmx-users] Adsorption energy of a single molecule

2009-11-12 Thread Darrell Koskinen
Hi Mark, No, I am not trying to build a random number generator and hope that I am not moving in this direction : ) My definition of adsorption energy would be the difference in energy when two species are at an infinite distance and the energy when these species are at an equilibrium distanc

Re: [gmx-users] Constraints & Restraints

2009-11-12 Thread Justin A. Lemkul
Darrell Koskinen wrote: Thanks for the additional comments. So given that, in my system, I have H atoms attached to C atoms on the perimeter of a finite graphene sheet that is placed above multiple infinite layers of graphene (graphite), would it be more appropriate to use: (i) a classical

[gmx-users] Constraints & Restraints

2009-11-12 Thread Darrell Koskinen
Thanks for the additional comments. So given that, in my system, I have H atoms attached to C atoms on the perimeter of a finite graphene sheet that is placed above multiple infinite layers of graphene (graphite), would it be more appropriate to use: (i) a classical (harmonic) model using cons

[gmx-users] free energy calculation using TI

2009-11-12 Thread Zhale Ghaemi
Dear all, I have a covalently bond ligand to a protein which its c=c bond could stay in Cis-enamine or Trans-enamine (I relaxed the structures of those two using classical MD in Gromacs4). I'm calculating the free energy difference of the Cis and Trans states using thermodynamic integration impleme

[gmx-users] Density histogram in Ramachandran plot

2009-11-12 Thread ms
Hi, I wonder if there is an easy way I am missing to get a density histogram from the Ramachandran plot over a trajectory as outputted by g_rama. All I see are big, uniform black blobs and they're not helpful, because with tons of data points a density plot would be much more informative. Thanks!

Re: [gmx-users] Hydrogen bond occupancy for the dimer of Acetic Acid

2009-11-12 Thread Ran Friedman
Hi Rasmus, >From your previous email I understood that you have only two molecules (you didn't write that you're using 500 and nothing on the rest of the system). Apparently, this is not the case. I don't think you can get what you want from g_hbond without modifying the source code. If you don't

Re: [gmx-users] Hydrogen bond occupancy for the dimer of Acetic Acid

2009-11-12 Thread Rasmus "Termo" Lundsgaard
Hi Ran. If I understand you right, then you suggest to have one molecule as acceptor, and the rest (499) as donors, and then look in the hbnum.xvg to see how often there is two hydrogen bonds... 1. is that I have to do this check for every molecule. 2. there is no guaranty that the two hydro

Re: [gmx-users] Hydrogen bond occupancy for the dimer of Acetic Acid

2009-11-12 Thread Ran Friedman
Hi Rasmus, A simple solution would be to run g_hbond twice, with two separate groups for acetate 1 as donor and acetate 2 as acceptor or vice versa, check the existence an hydrogen bond with g_hbond -num and write a script to check when the two hydrogen bonds co-exist. Hope that helps, Ran. Rasm

[gmx-users] Hydrogen bond occupancy for the dimer of Acetic Acid

2009-11-12 Thread Rasmus "Termo" Lundsgaard
Hi All. I'm trying to calculate the Hydrogen bond occupancy when there is two hydrogen bonds between same two acetic acid molecules at the same time. With g_hbond I can get the hbond.ndx giving me "all ocuring hydrogen bonds" group and the hbmap.xpm gives me the matrix of when these hydrogen

Re: [gmx-users] Constraints & Restraints

2009-11-12 Thread Ran Friedman
Erik Marklund wrote: > Mark Abraham skrev: >> Darrell Koskinen wrote: >>> Hi Tsjerk, >>> So then, if I understand correctly, setting "constraints = >>> all-bonds" is not as realistic as setting "constraints = none", >>> since the latter will allow for flexible (e.g. harmonic) behavoir >>> which is

Re: [gmx-users] LJ scaling and EnerPress correction

2009-11-12 Thread Mark Abraham
Antonia V. wrote: > > I am trying to simulate a two component system, and I would like to ask > > you the two following questions: > > > > 1) Is it possible to use a different scaling factor (for the LJ and the > > electrostatics) for each component? > > Not natively. How would you li

Re: [gmx-users] Constraints & Restraints

2009-11-12 Thread Erik Marklund
Mark Abraham skrev: Darrell Koskinen wrote: Hi Tsjerk, So then, if I understand correctly, setting "constraints = all-bonds" is not as realistic as setting "constraints = none", since the latter will allow for flexible (e.g. harmonic) behavoir which is more realistic than fixing the bond to a

Re: [gmx-users] Docking with PyMol and using Gromacs

2009-11-12 Thread Gunnar Widtfeldt Reginsson
This is exactly what I thought. I found out that saving the file with .mol ending in PyMol does not give the unwanted bonds. Thank you all. On Thu, Nov 12, 2009 at 8:49 AM, Ran Friedman wrote: > With VMD it's even simpler: use "dynamic bonds". > > Ran. > > Nicolas Sapay wrote: > > > > > > Dall

RE: [gmx-users] LJ scaling and EnerPress correction

2009-11-12 Thread Antonia V .
> > I am trying to simulate a two component system, and I would like to ask > > you the two following questions: > > > > 1) Is it possible to use a different scaling factor (for the LJ and the > > electrostatics) for each component? > > Not natively. How would you like to treat non-bonded int

[gmx-users] membrane protein tutorial information

2009-11-12 Thread irene farabella
Dear all, I am busy following the EMBO tutorial on membrane proteins (http://www.dddc.ac.cn/embo04/practicals/9_16.htm) but it is 2 days now that the server is down. Does anybody maybe know another url where I can find this tutorial? Thanks! Irene -- gmx-users mailing listgmx-users@gromacs.o

Re: [gmx-users] Docking with PyMol and using Gromacs

2009-11-12 Thread Ran Friedman
With VMD it's even simpler: use "dynamic bonds". Ran. Nicolas Sapay wrote: > > > Dallas B. Warren a écrit : >> >> Coordinate files like pdb and gro aren’t used by GROMACS to provide >> any bonding information. That is what the topology files are for. So >> their “presence” in your pdb isn’t an is

Re: [gmx-users] Docking with PyMol and using Gromacs

2009-11-12 Thread Nicolas Sapay
Dallas B. Warren a écrit : Coordinate files like pdb and gro aren’t used by GROMACS to provide any bonding information. That is what the topology files are for. So their “presence” in your pdb isn’t an issue. Actually, what is probably happening is that PyMol is guessing the bonds presenc