[gmx-users] How to calculate chemical shift?

Dear gmx users: I would like to calculate chemical shift using g_chi ,but the result has only : *** Chemical shifts from the chemical shift index *** PLEASE READ AND CITE THE FOLLOWING REFERENCE D. S. Wishart and A. M. Nip Protein Chemical Shift Analysis: A Practical Guide Bioche

Re: [gmx-users] analysing of the long trajectories

trjconv -dt use dt flag with the utility trjconv Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Jun 15, 2012 at 12:07 PM, a a wrote: > try ptraj > > -- > Date: Fri, 15 Jun 2012 10:18:40 +0400 > Subject: Re: [gmx-users] analysing of the long trajectori

Re: [gmx-users] Insertion protein in the membrane via G_membed

I've found main reason of such crushes. It was due to the individual internal waters wich I've included to my model as the buried to the protein interiour ( the coordinates were copppied form X-ray structure of the same protein). By the way I have already performed the same simulation with the in

RE: [gmx-users] analysing of the long trajectories

try ptraj Date: Fri, 15 Jun 2012 10:18:40 +0400 Subject: Re: [gmx-users] analysing of the long trajectories From: jmsstarli...@gmail.com To: gmx-users@gromacs.org By the way, I'm also looking for a most trivial way for extraction of pdb files from my trajectory on the desired intervals. E.g I

[gmx-users] current directory files

Dear All, In my protein pdb file I have changed some of the amino acid residue names. So accordingly I have changed corresponding residue names in force filed files and kept all the files [ modified and unmodified ] in my current working directory. Those files are 1) atomtypes.atp 2) amino

Re: [gmx-users] analysing of the long trajectories

By the way, I'm also looking for a most trivial way for extraction of pdb files from my trajectory on the desired intervals. E.g I have trajectory consisted of 5000 frames and I want to obtain 10 pdb files every each 500 frames ( or selected time interval as the alternative ). Commonly I do it ma

[gmx-users] simulating dimer proteins

Dear Gromacs users I want to compare some properties of two Interferons via MD simulation. One comes with pdb ID : 1ITF. (It has 24 Models in single pdb file, but each model with single chain.) I did pdb2gmx on this. The other is with pdb ID of : (1RFB). This has two chanis --

Re: [gmx-users] analysing of the long trajectories

Hi Tsjerk ! I my case I want to compare large-scale dynamics with more local events like fluctuation of the individual side chains so I suppose that I need larger number of frames. But how exactly I could define this number for my 100ns trajectory? Commoly I've used 5000 value for all nst* options

Re: [gmx-users] FEP

Hi Fabian, I am trying something similar with Glutamate to Alanine mutation. Does your dummy atoms i.e., DUM1 have a value of 0.0 for sigma and epsilon during all three steps or only in step 2? Thanks for the time, Sai On Thu, Apr 26, 2012 at 10:43 AM, Fabian Casteblanco < fabian.castebla...@gma

[gmx-users] RE: Re: g_lie reproducibility

Hi Mark, Thanks for the catch on the transcription error, I think I have found it ::embarrassed::. The repeated final value is still perplexing me. I have checked both my .xvg from g_energy and the .edr file with gmxdump. In both cases the final step (time value) only occurs once, and the second

[gmx-users] Bootstrapping using g_wham

Hi, I am currently using bootstrapping in g_wham to estimate the uncertainty in my PMF. I use a number of 1000 bootstraps. /software/gromacs/gromacs-4.0.7-plumed-1.2.0-x86_64/bin//g_wham \ -ip gwham.dat \ -bins 5000 \ -hist histo.xvg \ -bsres bsResult.xvg \ -nBootstrap 1000 This process

[gmx-users] Force constant in g_wham

Dear gmx-users, I am writing to clarify that the force constant kappa for g_wham corresponds to K_i itself, and not the quantity (1/2)*K_i in the umbrella potential W_i(ξ) = (K_i/2)*(ξ-ξ_i)^2. I recall reading somewhere that the force constant sometimes includes the (1/2) term in front of K_i,

[gmx-users] Diameter of the micelle

You first need to obtain an .xtc in which the micelle is entirely within the unit cell in every frame: http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering You can then use g_gyrate to get the radius of gyration or g_rdf to get the radial distribution function from the micelle COM o

[gmx-users] Diameter of the micelle

Hi, I am working with an emulsion water/n-dodecane in a box of 29nm. I wish to know how I can to get the diameter of the micelle in the frame, then I need to measuring the average diameter of the micelle in each frame. Thanks for your help!! -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] dodssp segmentation fault SOLVED for DEBIAN

Indeed, I am still using Gromacs-4.5.5, downloaded from gromacs.org on Debian GNU/Linux 6.0.5 (48-core AMD64) with kernel 3.1.1 and patched do_dssp manually as has been done for the newer releases. Works fine with the new dssp-2.0.4 release. raf On Thu, 2012-06-14 at 13:39 +0200, Erik Marklund

Re: [gmx-users] dodssp segmentation fault SOLVED for DEBIAN

This issue has been resolved so the next official release of gromacs will be capacle of using the newer versions of dssp. Erik 14 jun 2012 kl. 12.57 skrev Denis Kazakiewicz: > Wow, just did that. > In Debian have to use 4.5.5-2 version of Gromacs from sid repository. > Still have to use the old

Re: [gmx-users] dodssp segmentation fault SOLVED for DEBIAN

Wow, just did that. In Debian have to use 4.5.5-2 version of Gromacs from sid repository. Still have to use the oldest dssp http://swift.cmbi.ru.nl/gv/dssp/HTML/dsspcmbi It was simply Gromacs issue with no ways around. And it woks:) Just wondering, What are other efficient ways of analyzing se

[gmx-users] dodssp segmentation fault

Hello Dear Gromacs users. This is many times discussed issue, however nothing seems to work so far do_dssp returns "Segmentation fault" It is the oldest version of dssp: dsspcmbi Gromacs 4.5.5 on Debian i386 I did use export DSSP=/path to dssp 1. What is possibly could be? 2. Any other efficien

[gmx-users] Re: Effect of vdwradii.dat

Thanks, Mark. I tried this and there is, indeed, no difference. Anna -- View this message in context: http://gromacs.5086.n6.nabble.com/Effect-of-vdwradii-dat-tp4998465p4998496.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gro

Re: [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation

On 6/14/12 4:06 AM, ms wrote: Ok, I tried some of your suggestions and the Coulomb-SR energies still fall down very quickly. I wonder if: On 13/06/12 16:59, Justin A. Lemkul wrote: 4. What happens when you use the Andersen thermostat? That's not implemented yet for CPU calculations (though i

Re: [gmx-users] Protein near the edges of simulation box

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Cheers, Tsjerk On Thu, Jun 14, 2012 at 10:26 AM, Shima Arasteh wrote: > > Dear gmx friends, > > I put a protein in a simulation box filled of water molecules and entered > the mdrun command. After the simulation, I fo

[gmx-users] Protein near the edges of simulation box

Dear gmx friends, I put a protein in a simulation box filled of water molecules and entered the mdrun command. After the simulation, I found the protein near one of the edges of the box and not in center. What is the problem? Anyone may suggest me? Does it mean that the simulation is meaning

Re: [gmx-users] (3x3) Hessian matrix without minimization

On 14/06/2012 6:10 PM, Hyuntae Na wrote: > Message: 1 > Date: Thu, 14 Jun 2012 17:19:51 +1000 > From: Mark Abraham > Subject: Re: [gmx-users] (3x3) Hessian matrix without minimization > To: Discussion list for GROMACS users > Message-ID: <4fd99097.90...@anu.edu.au> > Content-Type: text/plain; c

Re: [gmx-users] (3x3) Hessian matrix without minimization

Thanks. Best regards,-- Hyuntae > Mark > -- next part ------ > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120614/6dcbb483/attachment-0001.html -- gmx-users mai

Re: [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation

Ok, I tried some of your suggestions and the Coulomb-SR energies still fall down very quickly. I wonder if: On 13/06/12 16:59, Justin A. Lemkul wrote: 4. What happens when you use the Andersen thermostat? That's not implemented yet for CPU calculations (though it was recently pushed into the 4

Re: [gmx-users] protein near the edges of simulation box

On 14/06/2012 5:47 PM, Shima Arasteh wrote: Dear gmx friends, I put a protein in a simulation box filled of water molecules and entered the mdrun command. After the simulation, I found the protein near one of the edges of the box and not in center. What is the problem? Anyone may suggest me?

[gmx-users] protein near the edges of simulation box

Dear gmx friends, I put a protein in a simulation box filled of water molecules and entered the mdrun command. After the simulation, I found the protein near one of the edges of the box and not in center. What is the problem? Anyone may suggest me? Does it mean that the simulation is meaningles

Re: [gmx-users] Insertion protein in the membrane via G_membed

Mark, I've used commands provided in the G_membed manual g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000 or g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000 -zinit 1.1 -zend 1.0 -nz 100 In both cases I've obtained the same message There are 122

Re: [gmx-users] Re: Dihedral Constraints

Sorry for the last reply, I wrote turns with different sequences wrongly, it's actually the turn with different dihedral constraints. I searched the gromacs user list , where I found this link , regarding calculation of dihedral energy of selected residues. I want to know whether this method would

Re: [gmx-users] Insertion protein in the membrane via G_membed

On 14/06/2012 4:39 PM, James Starlight wrote: Dear Gromacs Users! I've forced with the problem durin insertion of my protein into pre-equilibrated bilayer via G_Membed. I've done all steps in accordance to the KALP tutorial ( I've oriented both membrane as well as the protein in the same dim

Re: [gmx-users] (3x3) Hessian matrix without minimization

On 14/06/2012 5:04 PM, Hyuntae Na wrote: Dear All, I want to get a hessian matrix without minimizing a protein molecule. Essentially, I want to get the 3x3 hessian matrice of each atom (which is the diagonal term of the 3n x 3n hessian matrix). Would you help me to get it? Check out manual

Re: [gmx-users] Re: Dihedral Constraints

On 14/06/2012 4:57 PM, bharat gupta wrote: I am not going to compare this with anything , I have to look for sequences and their corresponding energies and select the lowest scoring ones. You can't compare total energies of different sequences and get a meaningful answer. What's the differenc

[gmx-users] (3x3) Hessian matrix without minimization

Dear All, I want to get a hessian matrix without minimizing a protein molecule. Essentially, I want to get the 3x3 hessian matrice of each atom (which is the diagonal term of the 3n x 3n hessian matrix). Would you help me to get it? Thanks a lot. Best regards,-- Hyuntae