[gmx-users] entropy from eigenfrequency

Dear Gromacs Users, I was just wondering if the formula and the units which I use for getting the entropy is absolutely correct. The eigenfrequency (v) in cm-1 are obtained from eigenfreq.xvg.( GMX ver 4.0.7, using normal mode calculations) TS = [alpha/exp(alpha)-1] -  log[1-exp(-alpha)] wher

[gmx-users] COM restraint similar to distance restraints

Dear Gromacs Users, I was wondering if there is a way to implement the COM distance restraints (which I presently apply using pull, and setting pull-rate =0.0) in way similar to distance restraints defining the lower up1 up2 (i.e harmonic restraint with a flat well). Any suggestion will be appr

Re: [gmx-users] COM restraint similar to distance restraints

Sorry to bother you all once again. As there were no replies, I assume it is not possible to implement COM distance restraints in a way similar to distance restrains. nahren From: nahren manuel To: gromacs gromacs Sent: Monday, April 1, 2013 9:56 PM

[gmx-users] Force components on ATOM XX

Dear Gromacs Users, Is it possible to get the forces (components, x,y, z) acting on each atom from the simulation  or from the rerun. I need them to calculate the Hessian Similar to http://www.sciencedirect.com/science/article/pii/S0006349507715989 Best, nahren -- gmx-users mailing list

[gmx-users] center of box protein

Dear GMX users, I am trying to center my protein at the center of box using editconf. When I view the same using ngmx, the protein seems to lie outside the box neweditconf -f alapdb.pdb -bt cubic  -o boxpdb.pdb -c -center -0.156 -0.061 0.084 -d 1.5 this one works, but the molecule is shifted.

[gmx-users] Umbrella sampling COM distance

Dear Gromacs Users, I am trying to study the free energy of binding in a protein-ligand complex. I use the following pull input in my mdp file: ; Pull code pull    = umbrella pull_geometry   = distance  pull_dim    = N Y N pull_start  = yes   pull_ngroups    = 1 pul

[gmx-users] PMF when pulling in -Z direction

Dear Gromacs Users, I am trying to study ligand unbinding adopting Umbrella sampling (using Gmx 4.5.3). during my initial pull to generate configurations for umbrella windows I have pulled in the -Z direction, @ s0 legend "0 Z" @ s1 legend "1 dZ" 0.    7.37361    -0.33625 0.0200    7.37377

Re: [gmx-users] PMF when pulling in -Z direction

, approx. 1 ns runs in 5 windows) Best, nahren From: Justin A. Lemkul To: nahren manuel ; Discussion list for GROMACS users Sent: Friday, November 4, 2011 7:44 PM Subject: Re: [gmx-users] PMF when pulling in -Z direction nahren manuel wrote: > Dear Grom

[gmx-users] how to get Eigenvectors

Dear GMX Users, I performed an ANM calculation at  http://ignmtest.ccbb.pitt.edu/cgi-bin/anm/anm1.cgi It returned me eigenvectors  in the following format (where the second and third column represent first and second eigenvector) 1  0.010551 -0.048553 1 -0.022038 -0.042918  1  0.107906  0.045

[gmx-users] (no subject)

Dear GMX Users, I am wish to perform  a conformational transition simulation using coarse-grained models (SBM http://smog-server.org/). I wanted to apply flooding to explore the conformational transition and have open-close transition my trajectory. But what I find is that when I start from a o

[gmx-users] Conformational transition using essential dynamics

Dear GMX Users, I am wish to perform  a conformational transition simulation using coarse-grained models (SBM http://smog-server.org/). I wanted to apply flooding to explore the conformational transition and have open-close transition my trajectory. But what I find is that when I start from a o

[gmx-users] -center -fit dodecahedron : dimer

Dear Gromacs Users,   I am performing a MD simulation of a dimer in a dodecahedron box. The simulation stopped after 8 ns (power cut) and i had to restart to complete it fully to 12 ns.   I then concatenated the two trajectories using trjcat   trjconv -f promd.trr -s proem.tpr -pbc nojump -o noj

Re: [gmx-users] -center -fit dodecahedron : dimer

Dear Gormacs User, I have now created a new tpr in which the protein is centered. trjconv -f promd.xtc -s tprdodecasolv.tpr -center -boxcenter tric -pbc mol -ur compact -o center.xtc trjconv  -s tprdodecasolv.tpr -fit rot+trans -f center.xtc -o fit.xtc I see the dimer getting split in some of th

[gmx-users] continue Prod run from NPT eq

Dear Gromacs Users, I am using ver 4.5.1. I completed a 500 ps run of NPT (the mdp file is below). after when i try to do a prod run with both velocity and pressure read from the output of NPT, I get a error newgrompp -f eq3npt.mdp -o eq3npttpr.tpr -p dimertop.top -c eq2nptpdb.pdb -t eq2npttr

[gmx-users] Translation motion during MD

Dear Gromacs Users, I am simulating a Membrane protein, the extracellular domain alone (since the structure of only extracellular domain is solved). So I will have to simulate the protein in such a way that only the translational motion is allowed but the rotational motions are prevented (which

Re: [gmx-users] Translation motion during MD

, 2010, 4:14 PM nahren manuel wrote: > Dear Gromacs Users, > > I am simulating a Membrane protein, the extracellular domain alone (since the > structure of only extracellular domain is solved). So I will have to simulate > the protein in such a way that only the translational motion is

[gmx-users] Residue Residue Contact

Dear Gromacs Users, I was wondering if there is a way in Gromacs to calculate the number of atoms involved in residue-residue contacts (within a given cut-off distance, say 5 A) over the entire trajectory. so if I have 100 residues and 500 frames, I would end with a 100X100X500 array (where 100

[gmx-users] Entropy by total atoms

Dear Gromacs Users, I am calculating entropy from QHA and Schlitters formula to determine the entropy change in my proteinA-proteinB complex. Since proA and proB are quite different in terms of number of residues, I am little confused if I should divide the entropy value with the number of atoms

[gmx-users] Porcupine Plots

Dear Gromacs Users,   I have done PCA of my MD , I want to visually represent the motions in terms of porcupine plots. I came across Dynamite (web server) for this purpose. But it only considers 500 frames of the xtc file. Is there any other way how i could generate porcupine plots based on tool

Re: [gmx-users] about dumping the last frame

Dear Awasthi, go through GROMACS Introductory tutorial... trjconv -f abc.pdb -s abc.tpr -o 3frame.pdb -dump 3 You can also open the pdb file in VMD and save only the last frame SIMPLE ! nahren --- On Mon, 2/2/09, Shirin Awasthi wrote: From: Shirin Awasthi Subject: [gmx-users] about dumping t

Re (in reply to Tsjerk): [gmx-users] Porcupine Plots

helps, Tsjerk On Mon, Feb 2, 2009 at 6:28 AM, Mark Abraham wrote: > nahren manuel wrote: >> >> Dear Gromacs Users, >> I have done PCA of my MD , I want to visually represent the motions in >> terms of porcupine plots. I came across Dynamite (web server) for this >> p

[gmx-users] how to parametrize Phos. Thr TPO

Dear Gromacs Users, I am trying to simulate a protein whose Thr residues is phosphorylated. I did the following based on the earlier query regarding the same here is how I did it for phosphorylated Threonine. 1) open the appropriate .rtp file e.g. ffG43a1.rtp 2) make a copy of the exi

[gmx-users] PBC dodecahedron (corrected)

Dear Gromacs Users, I am having some trouble in viewing my molecule in VMD as a protein in dodecahedron. I did the following 1.  trjconv -f promd.trr -o nojump.xtc -s promd.tpr -pbc nojump 2.  trjconv -f nojump..xtc -s promd.tpr -o mdcenter.xtc -ur compact -pbc mol -center -boxcenter tric I h

[gmx-users] Partial Vs Formal Charges

Dear Gromacs USERs, My ligand, which contains a piperazine ring & needs to be positively charged (+1). When I assign Gasteiger charges, it comes out to be -0.336 on the Nitrogen. But When I do a SEMI-EMPIRICAL PM3 to place my partial charge , it puts +0.733 on this atom. So does it mean it has

[gmx-users] Partial Charge of 1.11 ???

Dear Gromacs Users,     I calculated Partial Charges for my Ligand which is Positively Charged. When I Do a 3-21G* partial charge assignment based , I get partial charge value of 1.1147 on one of the Carbon atoms. I am little confused about it. can partial charges be greater than 1.???    Kindly

[gmx-users] Partial charges QM to GROMACS

Dear Gromacs Users,   1. I calculated the partial charges of my ligand using QM. Since GROMACS ignores the non-polar hydrogen, is it a good approximation to include the charges as it is from QM method to my ligand heavy atoms ?.   2.  should i adjust that partial charges , If so how to do the sa

Re: [gmx-users] Partial charges QM to GROMACS

ers] Partial charges QM to GROMACS To: [EMAIL PROTECTED], "Discussion list for GROMACS users" Date: Friday, July 11, 2008, 7:25 PM Quoting nahren manuel <[EMAIL PROTECTED]>: > Dear Gromacs Users, >   > 1. I calculated the partial charges of my ligand using QM. Since GROMACS &g

[gmx-users] Still :Partial charges QM to GROMACS

Dear Gromacs Users,  I think I did not frame my question correctly tha last time around. Sorry. Lets say for a C-H (alkyl) bond the partial charges ( from SEMI-EMPIRICAL) are (in bracket) C(0.234)-H(0.045) . so when I am using united atom ff such as GROMOS96 should I take the partial charges

[gmx-users] Seperate rlist - Coulomb & vdw

Dear Gromacs Users,   I just wonder if it possible to define   rlist = 0.9 rvdw = 1.2 vdwtype = cut-off rlist = 1.2   ; second rlist for rcoulomb coulombtype = cut-off rcoulomb = 1.5  I think  calulation wise it doen't make a big change , but just the idea striked me so wanted to know...   nahren

[gmx-users] ASP-LIG Interaction Energy : MDRUN

Dear Gromacs Users,   I have just completed one (5ns ) mdrun.   Now If i want to calculate the interaction energy between two residues, my ligand and ASP104, how should I go about calculating the same.   The one option I know is by creating .ndx . But I did not expect this residue to play an imp

Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

Dear Vivek, you just have to download swisspdb and open your pdb file. Thats all you got to do and It is more than enough. If you have more than 2/3 residues missing then, make sure the Ramachandran plots are fine. Also try a simple minimization before begining gromacs.   nahren --- On Tue, 8/1

[gmx-users] Trj conversion: ABCXYZ to AXBYCZ

Dear Gromacs Users, I simulated two homologous (proteins) , and noticed after the simulation that in one trajectory, the protein is stored as ABCXYZ and in another it is as AXBYCZ. (where A, Z are chain information, ABC is a trimer and XYZ

Re: [gmx-users] Trj conversion: ABCXYZ to AXBYCZ

2010 at 11:42 AM, nahren manuel wrote: Dear Gromacs Users, I simulated two homologous (proteins) , and noticed after the simulation that in one trajectory, the protein is stored as ABCXYZ and in another it is as AXBYCZ. (where A, Z are chain information

Re: [gmx-users] Trj conversion: ABCXYZ to AXBYCZ

) has   873 elements Group    16 (a_913-1368_a_2203-2619) has   873 elements Group    17 (a_1-456_a_1369-1785_a_457-912_a_1786-2202_a_913-1368_a_2203-2619) has  2619 elements Kindly advice nahren --- On Mon, 5/10/10, nahren manuel wrote: From: nahren manuel Subject: Re: [gmx-users] Trj

[gmx-users] Entropy from NMA

Dear Gromacs Users, I am trying to calculate Entropy from Normal Mode Analysis. I minimized the structure to 8.41750710592449e-09 Then I calculated the normal mode (the mdp file is given below). But when i try to calculate the Eigenvalues, I get the following warning One of the lowest 6 eigen

Re: [gmx-users] Entropy from NMA

0, Ran Friedman wrote: From: Ran Friedman Subject: Re: [gmx-users] Entropy from NMA To: "Discussion list for GROMACS users" Date: Wednesday, July 28, 2010, 3:10 PM p.s. How big is this negative value? Ran Friedman wrote: Hi, Can you post the exact commands you used for E

[gmx-users] Minimization before NMA

Dear Gromacs Users, I am unable to minimize a complex protein (Trimer-Trimer complex) to even less than Fmax=1.754e+00. I tried few tricks like performing MD for few steps etc, but it does not yield any results. I am sure there must be a way out. Can you please advice. Thanks for your attenti

Re: [gmx-users] Re: Minimization before NMA

Dear Gromacs Users, Thanks for your Reply. Yes i did move forward to calculate the eigenvalues, as listed below. 1 -1.0096 2   -0.860704 3   -0.621409 4  -0.0477899 5    -7.98079e-07 6    -2.20151e-08 7 2.76454e-06 8 0.000416762  

[gmx-users] intermolecular distance restrains

Dear Gromacs Users, I am presently using gromacs4.5 beta(since I want implicit solvent). I wish to apply intermolecular distance restraints. To my surprise there is no merge option in pdb2gmx (although pdb2gnx -h, says it has). So is there a new alternative to create intermolecular distance re

Re: [gmx-users] intermolecular distance restrains

--- On Thu, 9/2/10, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] intermolecular distance restrains To: "Discussion list for GROMACS users" Date: Thursday, September 2, 2010, 8:09 PM nahren manuel wrote: > Dear Gromacs Users, > > I am presently us

Re: [gmx-users] intermolecular distance restrains

le: pdb2gmx.c, line: 655 Fatal error: Atom OXT in residue LEU 427 was not found in rtp entry LEU with 19 atoms while sorting atoms. The residue are not in sequential Order , but i dont think that is the problem here. Thank you. Best, nahren --- On Fri, 9/3/10, Justin A. Lemkul wrote: From: Ju

[gmx-users] pdb2gmx -chainsep vs -merge

Dear Gromacs Users, Has anybody merged all chains in a PDB file using -chainsep. because -chainsep does not seem to work. http://www.mail-archive.com/gmx-users@gromacs.org/msg33192.html Is there a alternate way of doing it ?, One way I could think of is to add the atoms numbers in the  topologi

Re: [gmx-users] pdb2gmx -chainsep vs -merge

Dear Gromacs Users, thanks for all your suggestions. Tsjerk, I did try your idea, but unfortunately doesn't seem to work. the pdb file is shared here : http://www.4shared.com/account/file/ijofD83b/DIMER.html newpdb2gmx -f DIMER.pdb -chainsep interactive -ignh Fatal error: Atom OXT in residu

Re: [gmx-users] pdb2gmx -chainsep vs -merge

ject: Re: [gmx-users] pdb2gmx -chainsep vs -merge To: "Discussion list for GROMACS users" Date: Tuesday, September 7, 2010, 12:22 PM Hi Nahren, Can you paste your actual command line where you used sed? Cheers, Tsjerk On Tue, Sep 7, 2010 at 12:11 PM, nahren manuel wrote: Dear Gromac

[gmx-users] ARG Charmm gmx 4.5.1

Dear Gromacs Users, I am using plain cutoff for my 12-mer protein. The grompp reports ARG to have a big charge group. this was also highlighted in the following mail http://www.mail-archive.com/gmx-users@gromacs.org/msg32098.html I was just think if changing the charges on these atoms would help