[gmx-users] How do I monitor dynamics of helices and domain rotation?

Hi all, 1) I am looking at see if two adjacent helices are changing their conformation in space. I would like to monitor whether they are orthogonal to each other or have become parallel to each other during simulations. Is it possible in Gromacs to follow such changes, and if so, what command

[gmx-users] analysing helix dynamics

Hi all, During MD simulations of a protein,I find that there are two helices switch periodically from being parallel and perpendicular to each other. I'd like to plot out the orientation of these two helices with respect to each other, is there a command to extract this information? JJ

[gmx-users] Turning OFF/ON distance restraints during a simulation

Hi all, Is it possible to turn OFF/ON distance restraints after simulating a system for a certain period of time? If yes, how do I command GMX to do such a job? Thank you James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) -- gmx-users mailing listgmx-users

[gmx-users] distance restrained D simulations

output from other processes, depending on exactly when Open MPI kills them. -- -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] distance restrained D simulations

up with the same problem :(( On Sep 29, 2010, at 5:35 PM, jayant james wrote: Hi! I am trying to perform distance restrained MD simulations of a protein with Gromacs4.0.5. I have a bunch of FRET distances ranging from 10Angs to 40 angs that I am incorporating simular to NOE distance

Re: [gmx-users] CL atom not being recognised

gromos type [ impropers ] ; aiajakal gromos type [ dihedrals ] ; aiajakal gromos type On Mon, Jun 28, 2010 at 4:15 PM, Justin A. Lemkul jalem...@vt.edu wrote: jayant james wrote: Hi! The protein I am attempting to simulate has a CL atom. When I run pdb2gmx

[gmx-users] load imbalance

, Any help would be appreciated. Thank you Jayant James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search

[gmx-users] parts of protein unfolds during MD simulations

Hi! I have an issue with my protein modelling. I find that some of the helices (not all) have greatly unfolded during a 8ns distance restrained MD run. I am using the parameters below for the MD run. Is there any thing that can treat the system better than PME? thanks Jayant James title

[gmx-users] stopping and restarting a simulations after adding more constraints

grompp and later the mdrun command. The question is, Since I am restarting the simulation from 7ns I shoudn't give gen_vel=Yes. Am I right? Thanks Jayant James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing

Re: [gmx-users] handling particle decomposition with distance restraints

The energy minimization went on without any problem on 4 processors but the problem occurs when I perform the MD run. Also, I did not get any error message with relevance to LINCS etc... JJ On Wed, Jun 24, 2009 at 6:53 PM, Justin A. Lemkul jalem...@vt.edu wrote: jayant james wrote: Yes my

[gmx-users] handling particle decomposition with distance restraints

Hi! I am performing an mpi MD (on a quad core system) run with distance restraints. When I execute this command below without position restraints the MD run is distributed over 4 nodes perfectly well. But when I incorporate the distance restraints I hit a road block mpirun -np 4 mdrun_mpi -s

Re: [gmx-users] handling particle decomposition with distance restraints

) WARNING: Can not write distance restraint data to energy file with domain decomposition On Wed, Jun 24, 2009 at 5:10 PM, Justin A. Lemkul jalem...@vt.edu wrote: jayant james wrote: Hi! I am performing an mpi MD (on a quad core system) run with distance restraints. When I execute

Re: [gmx-users] handling particle decomposition with distance restraints

, Jun 24, 2009 at 6:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: jayant james wrote: I just replaced the old gmx 4.0 version with the 4.0.5 version and still the same problem NOTE: atoms involved in distance restraints should be within the longest cut-off distance, if this is not the case

Re: [gmx-users] mpi mdrun

/hostfile Thanks JJ On Wed, Jun 17, 2009 at 9:42 PM, Mark Abraham mark.abra...@anu.edu.auwrote: jayant james wrote: Hi! Oh!! I see that nnodes: 1. So does that mean that the job I gave is not running on four processors? If so how am I to solve this problem? You haven't configured your MPI system

Re: [gmx-users] mpi mdrun

Hi! After installing GMX without the mpi Igive the following commands make clean ./configure --enable-mpi --disable-nice --program-suffix=_mpi I am getting this problem when I give the --enable-mpi option checking build system type... x86_64-unknown-linux-gnu checking host system type...

Re: [gmx-users] mpi mdrun

...@anu.edu.auwrote: jayant james wrote: Hi !! I am attempting to install mpi mdrun such that I can use all four processors of my quad core system. But I keep running into this problem!! My operating system is Suse 10.1. (cd .libs rm -f libgmxpreprocess_mpi.la http://libgmxpreprocess_mpi.la ln -s

Re: [gmx-users] mpi mdrun

Hi! Oh!! I see that nnodes: 1. So does that mean that the job I gave is not running on four processors? If so how am I to solve this problem? thanks JJ On Wed, Jun 17, 2009 at 9:10 PM, Mark Abraham mark.abra...@anu.edu.auwrote: jayant james wrote: Hi Mark! Thanks for the tip I got

[gmx-users] mpi mdrun

Hi !! I am attempting to install mpi mdrun such that I can use all four processors of my quad core system. But I keep running into this problem!! My operating system is Suse 10.1. (cd .libs rm -f libgmxpreprocess_mpi.la ln -s ../libgmxpreprocess_mpi.la libgmxpreprocess_mpi.la) make[1]: *** No

[gmx-users] essential dynamics analysis

-- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please

Re: [gmx-users] energy

Hi! Thanks for your mail. I used two different operating systems and in both I found this problem of the energy file recurring!! Well I will go ahead and use the tpdconv to extend the simulations. Thanks JJ On Sun, Apr 5, 2009 at 4:38 PM, Mark Abraham mark.abra...@anu.edu.auwrote: jayant james

[gmx-users] energy

large nor the operating system not being able to write it, because the .trr file is much larger than this file and is being written down succedfully till 1000ps. I am using GMX 4.0. I welcome any suggestions on how to extend the MD run and to overcome this energy file problem. Thanks Jayant James

Re: [gmx-users] Simulated annealing

-phosphorylated serine) from the Non-Protein group. The Non-Protein group contains about 20,000 atoms (water, counterions and also the SEP group). So how can I remove this group from the Non-Protein group? Welcoming your suggestions Jayant James On Sat, Mar 21, 2009 at 4:52 AM, Justin A. Lemkul

[gmx-users] Simulated annealing

#tpbconv -s ../pr.tpr -f 300.xtc -e ../ener.edr -o 1ns.tpr -until 1000 #mdrun -s 1ns.tpr -o 1ns.trr -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org

Re: [gmx-users] Simulated annealing

annealing for the appended NMR group? Thanks Jayant James ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein Non-Protein ; Pressure coupling

Re: [gmx-users] Simulated annealing

, 2009 at 4:47 PM, Justin A. Lemkul jalem...@vt.edu wrote: jayant james wrote: Hi! I have a question with regard to a system that I am attempting to model. The N-terminal of chain of the protein was not resolved crystallographically but was later solved by NMR. Now my plan is to append

Re: [gmx-users] energy file

, 1481C 38,1 Top On Wed, Feb 25, 2009 at 11:03 PM, Mark Abraham mark.abra...@anu.edu.auwrote: jayant james wrote: Hi! I ran a simulation for 1ns (it was a continious run) and when I analyse the system energy, I find that the energy file has input till only 500pico seconds. Now that I

[gmx-users] Simulated annealing

Hi! I have a question with regard to a system that I am attempting to model. The N-terminal of chain of the protein was not resolved crystallographically but was later solved by NMR. Now my plan is to append the NMR structure on to chain A of the protein and perform simulated annealing only for

[gmx-users] energy file

-- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't

[gmx-users] checkpoint

Proper Dih. Improper Dih. LJ-14 5.97995e+037.39308e+033.31574e+032.12446e+031.21354e+03 md.log 634L, 23758C550,0-1 87% -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp

[gmx-users] LINCS warning

Hi! I am getting a message in the MD log file as below with respect ro LINCS mentioning deviations. I have constrained all bonds but this problem seems to pertain to a water molecule. Please suggest a way to oversome this issue. Thanks Jayant James Initializing LINear Constraint Solver number

Re: [gmx-users] restraining Ca2+ ion

= equal Thanks Jayant James ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests

Re: [gmx-users] restraining Ca2+ ion

for simulations in GROMOS96 force field found in GROMACS package. Thanks JJ On Wed, Jan 7, 2009 at 3:07 PM, Justin A. Lemkul jalem...@vt.edu wrote: jayant james wrote: Hi! In the protein of my interest I find that oxygen atoms of Thr, Tyr and Ser are close to the bound Ca2+. So is there any

Re: [gmx-users] restraining Ca2+ ion

Hi! Thanks for the reply. So would Gromos96 53a6 be available in the latest version of GROMACS? I am currently using Gromacs version 3.3.3. Thanks JJ On Wed, Jan 7, 2009 at 4:28 PM, Justin A. Lemkul jalem...@vt.edu wrote: jayant james wrote: Hi! Thanks for the reply. I am using the option

[gmx-users] phi/psi

. Is there some thing like this in GMX which I can specify in the *.mdp file? Thanks Jayant James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman

[gmx-users] restraining Ca2+ ion

the ca2+ in space hindering the spacial movement of that particular area!! but I am wondering if distance restraining of the ca2+ to the adjacent residues would be fine? or is there any other/better strategy? Awaiting your suggestions. Thanks Jayant James -- Jayasundar Jayant James www.chick.com

Re: [gmx-users] restraining Ca2+ ion

Hi, Thanks for your suggestions. Please take a look at the mdp file that I am using. Please suggest any changes that you feel would be adequate if the electrostatic treatment is poor. Thanks Jayant James ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file

[gmx-users] RMSD between

hi ! I am interested in plotting the RMSD between two amino acids to see if they come close or move away during simulations. Any suggestions would be helpful. Thanks Jayant James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp

Re: [gmx-users] how to distancing the counter ions from the protein?

well it seems to be on the protein's surface is it OK? On Mon, Jun 9, 2008 at 6:08 PM, Mark Abraham [EMAIL PROTECTED] wrote: jayant james wrote: Hi! I had to incorporate a salt conc of 0.15M NaCl and once I have them in put in the the box,via genion, I find that they are in close proximity

[gmx-users] how to distancing the counter ions from the protein?

Hi! I had to incorporate a salt conc of 0.15M NaCl and once I have them in put in the the box,via genion, I find that they are in close proximity to the protein. Is it possible to keep them away from the protein because I do not want them so close !! Thanks Jayant -- Jayasundar Jayant James

[gmx-users] calculating ionic strength

Hi all !! I want to add 150mM KCl into a cubic box that contains a protein in an aqueous environment. How am I to calculate as to how? many Ions of K and Cl, I need to add to bring to the above said salt conc? Thanks Jayant -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01

[gmx-users] protein molecule fragmenting after addition of counter ions

sulphur atoms ) have be yanked out of the protein! I wonder why this is happening!! Is there a way to rectify this? Thanks Jayant James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users

[gmx-users] distance restrained energy minimisation

2824 1 6 1 47 47.157 1.0 ~ Any tips to overcome this problem is welcome. Thanks Jayant James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) ___ gmx-users mailing listgmx-users

[gmx-users] ngmx crash

--- -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) Residence -24935864, cell-9841042164 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] position and distance restraining

Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) Residence -24935864, cell-9841042164 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

Re: [gmx-users] recognising phos group

Cheers, Tsjerk On Wed, Apr 9, 2008 at 3:44 AM, jayant james [EMAIL PROTECTED] wrote: Hi ! I am attempting to simulate a protein that is phosphorylated below is a part of the PDF file HETATM 460 P PO3 A 200 14.995 1.523 4.011 1.00 0.89 P HETATM

[gmx-users] recognising phos group

-- I do know that DNA can be simulated in GROMOS (option 0 of pdb2gmx). So I am wondering how to overcome the above error. Awaiting suggestions Thanks Jayant -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) Residence -24935864, cell-9841042164

[gmx-users] To the GMX developers-distance restraints

gen_vel=yes in em.mdp is this option possible . Thanks Jayant -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) Residence -24935864, cell-9841042164 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org

[gmx-users] table-extension

*hi ! I am getting this error with regard to table extensions. Any suggestions to overcome this would be greatly appreciated! Thanks Jayant James * Warning: 1-4 interaction between 429 and 434 at distance 1.002 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest

[gmx-users] Position restraint and distance restraints

specified every thing correctly. I have pasted essential parts of the topology file, em.mdp, pr.mdp, disres.itp and posres.itp. Awaiting your feedback Thanks Jayant James * *TOP FILE* ; Include Position restraint file #ifdef POSRES ;include posre.itp #endif ;includedisres.itp ; Include water topology

[gmx-users] enabling threads in GROMACS

hi all IS it possible to enable threads in gromacs during configuration? Thanks Jayant Jayasundar JayantJames Postdoc, Department ofVeterinary andComparative Anatomy,Pharmacology andPhysiology(VCAPP), Washingtonstate university,Pullman 99164-6520,USA.

[gmx-users] binutils error msg x86_64-unknown-linux-gnu

hi friends, I am installing GMX on a 2xdual core opteron processor system running on linux 10.0 I install lam by disabling the fortran as ./configure -without-fc make make install I configure fftw ./configure --enable-floats --enable-mpi make make install distclean ./configure --enable-mpi

[gmx-users] position restrained energy minimization

Hello gmx-users! 1. Is it possible to perform position restrained energy minimisation? 2. If so what are the parameter that I need to incorporate in the em.mdp file. By just changing the define = -DFLEX_SPC in the em.mdp to define = -DPOSRES will it mean that I am now entering into position

[gmx-users] failed dependencies

hi ! I am trying to install GMX on a opteron 2xdual core processor. OS- Suse Linux10.0. I actually installed the intel fortran compiler as I was just not able to get the Suse fortran compiler. I downloaded the suse 10 from opensuse.org. I get this message while trying to install lam error:

[gmx-users] GMX on 2xopteron Dual core

Hello friends! After reviewing the chart for GMX performance I purchased this 2x dual core opteron ,2.6GHz procesors and installed Fedora Core 4 (K8N-DL mother board). On booting up, the OS gives the message 'MP system not assigned by PSB bios structure. how do I overcome this problem? Would

[gmx-users] Simulations to corroborate FRET data

Hi all! I am performing simulations to corraborate with FRET data. I have performed mutations on a few residues and made them cys. To these cys AEDANS needs to be attached. The pdb O/P was got from PRODRG. Now my worry is how am I gonna build the .top file for this flour and how to attach it to

[gmx-users] missing residues

Hi friends! Part of a molecule that I am trying to simulate is not crystallographically resolved. To be exact about 17 amino acids from 136-148. Please suggest suggestions on how? I go about building these missing residues and integrating with the crystallographically resolved structure such that