Re: [gmx-users] Eessential dynamics analysis

Hi Sunita, It's a bit hard to understand exactly what you're dealing with. It would be helpful if you could link to or attach (leightweight) figures, illustrating what is going on. On a general note, I would suggest to read some texts about principal component analysis, from a statistical/mathema

[gmx-users] Eessential dynamics analysis

Dear friends, I performed essential dynamics (ED) analysis on my peptide using g_covar and g_anaeig. The first two eigenvectors represent 58% of the total positional fluctuation. The projection of the trajectory on eigenvectors gives me the proj.xvg file. From which I extracted the projection alon

Re: [gmx-users] Re: Can I run BD in water media using Gmx? (H.J.Risselada)

On Thu, 11 Jan 2007 09:50:12 +0800 "Hu Zhongqiao" <[EMAIL PROTECTED]> wrote: Thanks, Mark and Jelger, To Jelger, But If one can run BD by setting integrator=sd, how is dielectri constant of water set in the simulation? On p141 of the Manual v3.3, there is one option epsilon_r. Does it mean

[gmx-users] Re: Can I run BD in water media using Gmx?(H.J.Risselada)

Thanks, Mark and Jelger, To Jelger, But If one can run BD by setting integrator=sd, how is dielectri constant of water set in the simulation? On p141 of the Manual v3.3, there is one option epsilon_r. Does it mean BD can be run successfully if epsilon_r is set as ca. 78 for water? zhongqiao

Re: [gmx-users] 2 questions: pdb2gmx and genbox

WILLIAM R WELCH wrote: In the tutorial files I obtained in gromacs 3.3, on if I use pdb2gmx with no file specified, I get the input/output error an with the words "eiwit.pdb" So if I specify a pdb file, I get the error " invalid argument". What am I supposed to type on the command line to ge

[gmx-users] 2 questions: pdb2gmx and genbox

Hello, I am a brand new gromacs user--I have been banging my head against the wall with the manual for some time, so if someone could be so gracious, I have 2 simple questions: In the tutorial files I obtained in gromacs 3.3, on if I use pdb2gmx with no file specified, I get the input/output er

RE: [gmx-users] the box margin plot in VMD

You are best off asking this on the VMD emailing list. However, there isn't a function currently to do that. Best option that I have found is a script (available on the VMD website) that draws a box around the limit of the atoms/molecules within the box. Which doesn't do too bad of a job if ther

Re: [gmx-users] Re: Can I run BD in water media using Gmx? (Hu Zhongqiao)

On Wed, 10 Jan 2007 17:36:10 +1100 Mark Abraham <[EMAIL PROTECTED]> wrote: Hu Zhongqiao wrote: Hi, Nobody implied me till now. So that means the current version can not do BD by implicitly treating water into continuum media, i.e, use of dielectric constant of water. I hope Gmx developers

[gmx-users] Essential Dynamics Sampling (EDS) MD

Dear all, I'm trying to run MD with ED sampling. The target structure is a protein taken from one simulation, the .tpr file is taken from a different one. I'm using a subset of the CA atoms to calculate the eigenvectors. The problem is that the MD run crashes after set-up. Depending on the machin

[gmx-users] g_energy and/or g_enemat

Hi, I have doubts in as to use g_energy and/or g_enemat to calculate the free energy of a molecule (1JNR.pdb)reductase of the APS. I made two dynamic the temperatures of 300K and 311K.Waht´s the best option enters these two programs for the calculation? The calculated energy is stabilization energ

[gmx-users] negative diffusion constant by g_msd -mol option

Hello all, I calculate diffusion constant for each individual molecule using g_msd and -mol option. There are some negative values in the output file. Diffusion constant is always positive value, isn't it? I don't know how negative value is calculated. I am using gromacs 3.2.1. give me some advi

[gmx-users] g_sdf function in a 2D map

Hi to All! I am using the g_sdf and g_rdf functions to analyse the solvation of some molecules. With g_sdf I get nice 3D maps that describe the g_rdf ... however I would like to know how is it possible to produce 2D maps from these files (with contour lines for example). I am using Chimera t

Re: [gmx-users] energy

hi, On Wednesday 10 January 2007 09:45, mahbubeh zarrabi wrote: > Dear all > how can I calculate interaction energy in complex with > gromacs > best wishes yuo can define energy groups in your mdp file rerun your calculation (mdrun -rerun ...) and than extract them with g_energy. The number of

Re: [gmx-users] energy

> Dear all > how can I calculate interaction energy in complex with > gromacs Start by writing down an algebraic expression for what you want to calculate in terms of things you might be able to compute with an MD simulation. If you can do that, then please ask a focussed question. Otherwise you s

[gmx-users] energy

Dear all how can I calculate interaction energy in complex with gromacs best wishes Need a quick answer? Get one in minutes from people who know. Ask your question on www.Answers.yahoo.com _

Re: [gmx-users] The meaning of rlist and rcoulomb for coulombtype=reaction-field

Does this 0.25 nm buffer get automagically added to the specified rcoulomb to determine the neighbor searching radius? No, I checked, and that doesn't happen in src/mdlib/ns.c My guess is that the actual implementation includes all atoms in charge groups that have at least one atom inside the r

Re: [gmx-users] The meaning of rlist and rcoulomb for coulombtype=reaction-field

Mark Abraham wrote: I am having a difficult time understanding the meaning of 'rlist' and 'rcoulomb' when the reaction-field treatment of electrostatics is used. After explaining the twin-range cutoff method (which seems to be fairly straightforward) which explains the case where rlist < rcoulom