Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 106

Dear Sabuj,   It would be difficult to help without more info (size of system, contents of system, .mdp file, etc...).  I have not used simulated annealing in years, and when I used the software in the past, it was mostly structure determination from unknown phases (cooling an unknown partial st

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 93

Dear A.S. Lacey,   Along the lines of Justin's answere, you need to perform more complicated simulations.  I would suggest the 54a7 (partial atom) or CHARM36 (all atom) force fields, and add solvent and ions in a simulation box.  Once in equilibration, your structure should mimic something like

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 93

Dear Ganesh,   You can also use the ATB site, and convert the all atom .itp to CHARM36 format, or build it (charge, bond, angles, etc...) from the already present CHARMM36 atom parameters.  Check your charges if you get them from the ATB.   Stephan Watkins   On 1/22/16 8:51 AM, Ganesh Shahan

Re: [gmx-users] conserved energy

  You should also understand energy at the atomic level, the standard atom-atom inteeractions from general O chem, or chem suck as leonard jones and coulumb...per the standard, non-indexed outputs...they do not follow newtonian based energy systems even though the algorithm is newtonian based in m

Re: [gmx-users] Steered MD simulation of drug molecules across the plasma membrane in gromacs 5.0.4

Its seems to have changed from the versions I remember in the 5 (or maybe I remember wrong), I found you now have to use a - vector...geometry direction, I vaguely remember you could just use a - pull rate in the past...but then you can now use a single group and an absolute reference point...or d

Re: [gmx-users] calculating free energy

  In general a realistic unfolded system would have to start at several random points in state A, and allowing it to fold into state B.  This accounts for gaussian distributions of random states... these tend to be long as the folding process is between 200 (for short) to 5-6 usecounds for longe

Re: [gmx-users] trjconv_d errors

Thats what I thought.    I recieved no response, but can jimmy rigg the entire thing to be processed on 4.6.7 from a 5.0.1 run, however it looses the temperature?   Sincerely,   STephan L. Watkins, PhD   Gesendet: Montag, 06. April 2015 um 02:51 Uhr Von: "lloyd riggs"

Re: [gmx-users] trjconv_d errors

  Dear All,   I recentlly installed gromacs 5.0.1 and a few months later 5.0.4 (hoping there was adifference) as I am using terra grid with a 5.0.1 install.   Now, I noticed 2 things, trjconv_d no matter what I do can not read or convert the .trr file, even with simple -f in.trr -o out.trr or .

Re: [gmx-users] Umbrella Sampling and histograms smoothness

Funny,   I could but dont have time.  You should look at Uni Washington things...if your doing that I would say restrain one for 10 sims, then the other and see if there's differences, and publish something on differences for restraints...on A vs. B, which I have never seen...   Stephan Watkin

Re: [gmx-users] Axis

  Dear Gromacs users,   Is there a way to change the x y z axis as read by the software, in just the simple pdb/gro file?  I want to transpose the z onto x as read by the computer.   Stephan Watkins -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/

Re: [gmx-users] Version 12

I found it its 4.5.5,   Steve   Gesendet: Freitag, 31. Oktober 2014 um 07:42 Uhr Von: "Mark Abraham" An: "Discussion list for GROMACS users" Betreff: Re: [gmx-users] Version 12 Mdrun reports its version, yes? Mark On Oct 31, 2014 7:14 AM, "lloyd riggs&q

Re: [gmx-users] Version 12

  Im getting a "Attempting to read a checkpoint file of version 15 with code of version 12", does anyone know off hand which is version 12 ? Im guessing lik 4.5.6 , but dont know.   Stephan Watkins -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mai

Re: [gmx-users] Membrane simulations

Dear All,   So I have been doing membrane simulations on a small (really small) node for a few months, and was able to get in a few hundred nanoseconds of time.  I now have added 4 inositol lipids, and repeatedly encounter some errors as follows.   I set the time in the eq for 0.0005 and it ru

Re: [gmx-users] MD workstation

  Is there any progress in openCL versions of Gromacs, as it is listed on the developer site?  Just askin.  One thing I ran across is one can get integrated GPU arrays on a board if you find say Russian board designs from China for about the same price with 10x the computational speed, but the boa

Re: [gmx-users] g_mindist for hydrophobic interactions

  you should go down the list and use all the tools, and use some from seperate software.  In my experience, the trjconv gets rid of say 4-5 crazy single points in a graph based on a single point where one of the atoms or residues involved moves between planes, which averidge out in a gaussian dis

Re: [gmx-users] protein-ligand complex by gromacs

did you center everything, or are you just looking at it in VMD?   Gesendet: Montag, 08. September 2014 um 18:30 Uhr Von: "Mahboobeh Eslami" An: "gmx-us...@gromacs.org" Betreff: [gmx-users] protein-ligand complex by gromacs hi GMX users i have simulated the protein-ligand complex by gromacs.

Re: [gmx-users] centering with trjconv

I like the fit progressive sometimes more...   Stephan   Gesendet: Dienstag, 26. August 2014 um 21:49 Uhr Von: "Tsjerk Wassenaar" An: "Discussion list for GROMACS users" Betreff: Re: [gmx-users] centering with trjconv Hey :) What about -pbc nojump -center ? Cheers, Tsjerk On Tue, Aug 2

Re: [gmx-users] Membrane simulations

ctor 2014-08-13 0:58 GMT-05:00 lloyd riggs : > Dear GMX users, > > I ran across a nice web page, I believe from a brazilian group, for > generating membranes of any compnents (pdb). This was months ago, and after > a few days of trying, I cannot find the page again. It was capable

[gmx-users] Membrane simulations

Dear GMX users,   I ran across a nice web page, I believe from a brazilian group, for generating membranes of any compnents (pdb).  This was months ago, and after a few days of trying, I cannot find the page again.  It was capable of makeing bilayers, as well as other shapes, including small mic

Re: [gmx-users] specbond identified by pdb2gmx but not added to topology

never mind just found it in your input pdb sorry.  Is it at the end?   Gesendet: Samstag, 07. Juni 2014 um 16:32 Uhr Von: "Vedat Durmaz" An: "Discussion list for GROMACS users" Betreff: [gmx-users] specbond identified by pdb2gmx but not added to topology dear gmx users/team, i've defined some

Re: [gmx-users] specbond identified by pdb2gmx but not added to topology

Its probably a single atom name typo unless its the end residue ( I know from experience after 45 minuts or more, typos become extreemly difficult to spot for pshchological reasons), but you would need to show the in file (pdb) and probably the top for a spot check.   Stephan   Gesendet: Samst

Re: [gmx-users] Need some help with membrane simulation

Has anyone done an all atom 53a6 or 54a7 .itp/rtp that can be downloaded (reguarding protein/amono acids or and nucleic?  I can make one in a week (for proteins) just using a topology builder and modifying things, there are already lipids around 100 with all atom in either field, but after reviewi

Re: [gmx-users] New Molecule Topology

I think the Ausi ATB is a bit beter for initial topologies,but still needs some input afterwards.  They usually have less to change around needed, or beter charge sets, but tend to have problems with adding a hydrogen.  Only for 53a6 though.  Also, just loking at the ff topoloy you canput one toge

Re: [gmx-users] binding sites with MD

Theres one paper that shows (VMD film) and talks about diffusion times I know of, however I do not know of any simply looking for ligands via setting up an MD system, then running them long enough to see if they find a site, this seems like a large amount of excessive work as the systems are much

Re: [gmx-users] (no subject)

  I have an interesting question reguarding NH2 attached to cyclic rings in topology files.  I have seen them represented in a somewhat SP3 state, where the hydrogens are held as if there were almost 3, rather than two.  I have also seen them artificially flatened with an improper dihedral, which

Re: [gmx-users] entropy vs time plot

Yah but you'll have to smooth it, mean wise, or beter averidge several runs. qtiplot or equivalent will work (even MS Excell if you have the added mean determination formulas).   Stephan Watkins   Gesendet: Mittwoch, 21. Mai 2014 um 06:54 Uhr Von: "tarak karmakar" An: "Discussion list for GRO

Re: [gmx-users] GPU in Ubuntu

stable Linux for computational work. I recommend the following: Redhat Enterprise, Scientific Linux,SuSE Linux Enterprise Ubuntu is on not stable enough for professional work according to my own experiences. On 05/10/2014 10:06 PM, lloyd riggs wrote: > Dear All, > I recently ran into a p

Re: [gmx-users] GPU in Ubuntu

  Dear All,   I recently ran into a problem with a small geforce 610, and aside from woundering if it was worth the effort, found in Ubuntu 13.10 gromacs can not find the GPU.  The Nvidia site found this problem and states to install libcudart.5.5.so or higher, i tried this and the 6.0 as well,

Re: [gmx-users] PEG residue

You can get most of these tabulated in a CRC book, an older one is easier to read (circa <1988), online through the international union of physics and chemsitry web site(s), or look over the partial force field (54a7) and locate the same bonds/angles such as aminos and nucleic acids, as the sugar/

Re: [gmx-users] binding delta G, H and S for ion-protein

  Dear Board,   I have done this with a steered MD, using covarience, etc...in the end there are nice delG and H,S line graphs...the only argument I have heard however is when doing the subtraction the third curve always gives the correct repective energy change, but the delG line graph may not

Re: [gmx-users] MD SIMULATIONS ON A CLUSTER

Yes it is, or should be from my experience.  You need to look at the mailinglist, and it takes time t work out somethings as there also system (your simulation) dependent.  Mostly these are parameters such as domain decomposition sizes, number of threads, -rdd, -rcon -dds and others (I found more

Re: [gmx-users] pca

Suggestions,   You can look at your plots from g_sham in an editor, and simply cut/past then add the matricies portion in something like qtiplot/Scidavis, or you need to back track and use covarience in the gromacs auxillary scripts (g_covar/aneig, etc...) and track down some matrix scripts to d

Re: [gmx-users] Potential energy calculations

ot; An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] Potential energy calculations On 12/26/13, 4:52 PM, lloyd riggs wrote: > Yes I know what you mean, however when your looking over a unit cell and trying > to define a single molecule in the solvent (even as represented by the entire &

Re: [gmx-users] Potential energy calculations

reff: Re: [gmx-users] Potential energy calculations On 12/26/13, 5:30 AM, lloyd riggs wrote: > Zero it--> If you plot a potential energy value strait from the simulation it > will be something like point a) -7000 point b) -7050 across a single > simulation. Thus you have to find a

Re: [gmx-users] Potential energy calculations

  Also, if your not doing a diffusion type thing where half or a portion of one side of the box is DMSO and the other water, like say 100% DMSO but averidging, such as a random equilibrated solution of small molecules, the energy system will be sinusoidal, thus any energy plots vs. time will fluct

Re: [gmx-users] Potential energy calculations

Zero it--> If you plot a potential energy value strait from the simulation it will be something like point a) -7000 point b) -7050 across a single simulation.  Thus you have to find a beginning point and subtract it across the run.  Additionally, fluctuations may dictate 10 or so runs to determin

Re: [gmx-users] Potential energy calculations

Did you zero it ?   Stephan Watkins   Gesendet: Dienstag, 24. Dezember 2013 um 01:33 Uhr Von: virk An: gmx-us...@gromacs.org Betreff: [gmx-users] Potential energy calculations Dear Users, I am try to simulate DMSO molecules. I am getting potential energy values of Energy Average Err.Est. R

Re: [gmx-users] Bin files of g_sham

ique which can help me to look at the frames corresponding to the the energy? Meanwhile, I shall also try to grasp your advice/suggestions and see how far can I make my little brain work towards it. Kind regards, Ankita On Thu, Dec 19, 2013 at 2:49 AM, lloyd riggs wrote: > Trying to hel

Re: [gmx-users] Bin files of g_sham

has the following lines: > > [ 18 ] > 7105 > [ 19 ] > 7104 > [ 46 ] > 7124 > [ 48 ] > 7123 > [ 49 ] > 7106 > [ 50 ] > 6497 > 6498 > [ 51 ] > 6499 > 6500 > [ 52 ] > 6496 > 7103 > [ 53 ] > 7102 > [ 55 ] > 6672 > [ 75 ] >

Re: [gmx-users] Bin files of g_sham

e higher time scale. My simulation was for 48ns > and had 3fs time step. I am unable to trace anything beyond 22000 or 23000 > number in my bins. > > I hope you could help me solve this confusion. > > Kind regards, > > Ankita > > > On Sun, Dec 15, 2013 at 11:17 PM, ll

Re: [gmx-users] Bin files of g_sham

  I will attempt an answer, however there might be a better response.  It depends on your input .xvg (what the first column is) and what you are telling it to do (defualt is time), and if these correspond to your time frames (can be timepoint or siply frame # I believe).  g_sham seems (to me) to w

Re: [gmx-users] Atomistic Simulation

I've used the ATB, there kinda the replacment for the PRODGR, which is now commercial.  They do have the same problems though, such as 99% correct output, and then manual changes for something (example: an NH2 on the side of a ring parameterized as an NH3, so acts as such...needs to be changed, bu

Re: [gmx-users] Charge correction PME

Sorry to but in on the conversation.  Im between computers so cant track it down easy, (on my hard drive) but I did find one older publication comparing gromacs solvent (ion/buffers) effects with plasmon resonance calculated affinities, the results of that single paper showed the closer the solven

Re: [gmx-users] Normal Mode Analysis

r GROMACS users" Betreff: Re: [gmx-users] Normal Mode Analysis Hi Stephen, You're confusing NMA with PCA. Cheers, Tsjerk On Tue, Nov 26, 2013 at 6:30 AM, lloyd riggs wrote: > I don't know your energy break down, if you look at frames with g_anaeig > using -first and -last to

Re: [gmx-users] Normal Mode Analysis

Normal Mode Analysis Hi Stephen, You're confusing NMA with PCA. Cheers, Tsjerk On Tue, Nov 26, 2013 at 6:30 AM, lloyd riggs wrote: > I don't know your energy break down, if you look at frames with g_anaeig > using -first and -last to set your vector number(s), and then frames

Re: [gmx-users] Normal Mode Analysis

I don't know your energy break down, if you look at frames with g_anaeig using -first and -last to set your vector number(s), and then frames set to your time units desired, it will give you something you can look at with vmd or pymol.  I have noticed though after the frst 4 or so vectors, it beco

Re: [gmx-users] How can I tell whether or not Gromacs was compiled with MPI?

Try using the mpi submissions flags with just a test submission, you might have to look at the stats after 15 minutes though, as I do not know what would happen if it was not compiled with mpi (if they work or not), but they would make a noticable difference.   just a suggestion, there might be

Re: [gmx-users] cluster-PCA

Read The manual portion on covariance analysis, g_covar and g_anaig, it is pretty descriptive and answeres all your questions.   Gesendet: Freitag, 22. November 2013 um 19:20 Uhr Von: "Shine A" An: gmx-us...@gromacs.org Betreff: [gmx-users] cluster-PCA Sir, I did 200 ns MD simulation. Now I wan