[gmx-users] Distance Restraints

Hi, I'm new to Gromacs. How to convert NMR paramagnetic relaxation enhancement distance restraints into gromacs format in topol.top file for structural MD refinement. --Rama -- View this message in context: http://gromacs.5086.x6.nabble.com/Distance-Restraints-tp5008207.html Sent fro

[gmx-users] Distance restraints

Dear Gromacs users, How to define distance restraints between two molecules(protein and a lipid) in a topology file. Thanks.. -- View this message in context: http://gromacs.5086.x6.nabble.com/Distance-restraints-tp5008421.html Sent from the GROMACS Users Forum mailing list archive at Nabbl

[gmx-users] Stimulation stopped at 2ns

Dear All, I'm trying to do long stimulation run but every time it stops at 2ns, below pasted .mdp file parameters. How to run 10ns or more ns stimulation run? Do I need to change any parameters in .mdp file or else where. Thanks in Advance. - title = Protein-DMPC bilayer Pr

[gmx-users] snapshot

Hi, How to get a snapshots in equal intervals of time (250ps) from production MD trajectory. I'm using -sep , -t0, -timestep but output came only one .gro file. -- View this message in context: http://gromacs.5086.x6.nabble.com/snapshot-tp5009837.html Sent from the GROMACS Users Forum mailin

[gmx-users] How to make changes on Trajectory file?

Hi, I saved my coordinates every 500ps in production MD run, could I alter now .xtc file by saving different coordinates for ex: every 100ps. Is there any command to alter the files. Thanks in Advance --Rama -- View this message in context: http://gromacs.5086.x6.nabble.com/How-to-make

[gmx-users] DMPC Bilayer

somewhere else. --Rama -- View this message in context: http://gromacs.5086.x6.nabble.com/DMPC-Bilayer-tp5010685.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-user

[gmx-users] DMPC Bilayer

Hello, At NPT stage the two leaflets in DMPC bilayer is separated a while and comes closer. Is this common in this stage or any thing goes wrong in equillibration. Thanks --Rama -- View this message in context: http://gromacs.5086.x6.nabble.com/DMPC-Bilayer-tp5010783.html Sent from the

[gmx-users] NMR restrained MD

Hi, I'm doing NMR restrained MD simulation for protein-Bilayer system to satisfy NMR experimental data. Without restraints there is no problem, but if I include distance restraints in topology file, getting fatal error: the lipid atom index # was not recognized by using this command: g_grompp

[gmx-users] Distance calculation

Hi , I there any tool to calculate distance between particular atom from one group(protein) to particular atom from another group(DMPC lipid in Bilayer). For Example: protein backbone Amide(HN) to acyl chain carbon atom(C2D) in DMPC lipid. Thanks Rama -- View this message in context: http

[gmx-users] Broken lipid molecules

. How to fix whole MD trajectory? Thanks Rama -- View this message in context: http://gromacs.5086.x6.nabble.com/Broken-lipid-molecules-tp5011344.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

[gmx-users] Change in the positon of structural Zinc and calcium ions during MD

Hi Gromacs users, I'm doing protein-Bilayer MD simulations. Enzyme contains structural zinc and calcium ions during Energy minimization, NVT and NPT stage, ions are changing there position even though I applied position restraints for the atoms and ions. Anyone could help me out. Thanks -- Vi

[gmx-users] Re: Change in the position of structural Zinc and calcium ions during MD

Hi Justin, Below I pasted .mdp file and topology. In .log file I could see energy term for position restraints. .mdp file--- title = NPT Equilibration define = -DPOSRES ; position restraints for protein ; Run parameters integrator = md

[gmx-users] Fwd: how to add close proteins

Hi GROMACS users, I wish to study proteins behaviour,With the help of command genbox -ci protein.gro -nmol .. -box -o -pI am putting the four peptide at random positions, but I need to put theem close enough so they are forming at least one hydrogen bond or at least enough close to start in

[gmx-users] about protein in periodic boundary condition..

Hi GROMACS user, With the help of command genbox -ci -nmol -o -box I get the desired no of added protein to cell. But I found that some part of protein is outside the cell .. Is such system is good for further molecular dynamics study ...?? After energy minimis

[gmx-users] about periodicity removal

Hi GROMACS friends, I am trying to put to peptide close to each other.. with the help of -editconf -ci and -nmol option ,the peptide can be put randomly at different location, but they are far apart. To solve problem I proceed as follow... 1. I make gro file , with

[gmx-users] about periodicity removal....

Hi GROMACS friend, Thank you Justin For guidance. As I also doing your KALP-15 in DPPC tutorial, In that you maintain remove initial periodicity of DPPC.. What is means initial periodicity?? That is the reason I thought the peptides have Initial periodicity.(As periodic

[gmx-users] crashed run...

Hi GROMACS specialist, My MD run get crashed because of less memory. I given the command mdrun -s -f -e -o -g -cpi -append -v Now is my system is started from the initial time or from the time of crash?? What is the process for to start

[gmx-users] MDrun append...

Dear GROMACS Friends, my MD run get crashed , I foollow following command .. mdrun -s protein_md.tpr -c protein_md.trr -e protein_md.edr -g protein_md.log -cpi -append -v the system respond in a way.. Fatal error: The original run wrote a file called 'traj.trr' which is larger than 2 GB, but m

[gmx-users] LINCS Fatal error

Hi GROMACS specialist, I am using MARTINI forcefield, My mdp file contain following parameter constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 90 gromacs output is Step 0, time 0 (ps) LINCS WARNING relative constraint deviation

[gmx-users] Segmentation fault

Hi , Thank you for help. I solve my problem for LINCS error But now I have another problem after mdrun command gromacs output Making 1D domain decomposition 4 x 1 x 1 starting mdrun 'Martini system from nap.pdb' 5000 steps,100.0 ps. step 0Segmentation fault Please give the valuable sug

[gmx-users] About martini

Dear GROMACS specialists, How to convert Coarse Grain Martini to FG martini on Gromacs 4.5.4 version . ( And how to compile the source given in Martini home page with 4.5.4 version as they mention only Gromacs 3.3.1 version) Please give the valuable advice.. -- gmx-users mail

[gmx-users] protein-ligand tutorial problem

Hello     I am doing JUSTIN Protein-ligand tutorial. I complete your Lysozyme tutorial before these one. I complete tutorial upto the make-ndx but after giving command grompp for nvt.tpr production..  I get the following error No molecule were defined in the system , I know somewhere

[gmx-users] Regarding PCA

Hi Gromacs Specialist, 1. I need the help regarding the PCA (Principle component analysis ). If anyone can suggest me a good review article and some tips how to analyse PCA result I am very new to simulation study. I read GROMACS manual, but I need any review type article.

[gmx-users] Simulated Annealing Protocol...

Dear Gromacs Specialists, I am very novice to Molecular Simulation study. I am using GROMACS 4.5.4 version . I completed some GROMACS tutorials , I not found any tutorial on Simulated Annealing.. If Any one know the link please give me it.. I make my protocol to work on simulated

[gmx-users] Simulated Annealing Protocol...

ted... Thank you With Best Regards, On Fri, Mar 16, 2012 at 7:10 PM, Justin A. Lemkul wrote: > > > rama david wrote: >> >> Dear Gromacs Specialists, >>                I am very novice to Molecular Simulation study. >>  I am using GROMACS 4.5.4 version . >> I comp

[gmx-users] Erroneous bond in average pdb

Hi Gromacs Specialist, I want to study protein aggregation study. 1. after giving the command g_anaeig -v .. -s .. -f .. -first 1 -last 1 -nframe 100 -extr ev1.pdb I got the pdb structure having 100 frame , but the structure have erroneous bonds, I try both VMD and pymol, but but get the

[gmx-users] About center of mass removal

Hi Gromacs Specialist, I want to study How the protein interact with each other ?? I run one simulation with following MDP file option .. comm_mode = Linear; remove center of mass translation nstcomm = 1 ; [steps]

Re: [gmx-users] About center of mass removal

arning affect my run ...which proparty I have to check ?? Thank you in advance.. On Sat, Mar 24, 2012 at 9:41 PM, Mark Abraham wrote: > On 24/03/2012 11:06 PM, rama david wrote: > >> Hi Gromacs Specialist, >> I want to study How the protein interact >> with e

[gmx-users] About movie in GROMACS

HI Gromacs Friends, I complete one simulation for 4 different molecule placed apart in box of dimension 4 4 4 .. when I used the trajectory I saw the one molecule interact with each other but they are getting broken because of box..(Some part protruding from other side). To see movie

[gmx-users] about g_mindist....

Hi everybody , I run simulation of 4 same molecule keep apart in box of 4 4 4 dimension ..( 71 atom in one molecule = 71 * 4 = total atom are 284 ) force field = gromacs96 53a6 COM (center of mass) infirmation of molecules system size : 1.255 1.577 1.883 box vectors : 4.000 4

Re: [gmx-users] Shima Arasteh wants to share a link | Gromacs

Hi shima Read the insttruction carefully .. DELETE ALL THE LINE AND SUBSEQUENT LINES IN THE SECTION Delete all the bellow line in that section... It will surely solve your problem (As I also Face the same one ) with best wishes, On Thu, Mar 29, 2012 at 11:23 AM, ros...@kth.se

[gmx-users] About cutt-off scheme ..

Hi Gromacs users , as per the link given on gromacs website... Introduction to Molecular Dynamics Simulations and Analysis- Tutorial for performing and analyzing simulations of proteins. Includes examples of many of the gromacs analysis tools and addr

Re: [gmx-users] About cutt-off scheme ..

t 5:05 PM, Justin A. Lemkul wrote: > > > rama david wrote: > >> Hi Gromacs users , >> as per the link given on gromacs website... >> Introduction to Molecular Dynamics Simulations and Analysis < >> http://nmr.chem.uu.nl/%**7Etsjerk/course/molmod/&

Re: [gmx-users] about g_mindist....

29/03/2012 7:20 PM, rama david wrote: > >> Hi everybody , >> I run simulation of 4 same molecule keep apart in box >> of 4 4 4 dimension ..( 71 atom in one molecule = 71 * 4 = total atom are >> 284 ) >> force field = gromacs96 53a6 >> >&g

Re: [gmx-users] About cutt-off scheme ..

box boundary ,so they may close to each other enough .. so is the simulation is wrong or right ... 2. Please could you tell me , What are the right parameter for the G96 53a6 force field ?? thank you a lot for help .. On Thu, Mar 29, 2012 at 7:03 PM, rama david wrote: > Hi Gromacs frie

[gmx-users] Fwd: About g_energy analysis

-- Forwarded message -- From: rama david Date: Fri, Mar 30, 2012 at 8:31 PM Subject: About g_energy analysis To: Discussion list for GROMACS users Hi Gromacs users , I have 4 molecule in system, I am study how are they interacting , I did NPT, equilibration , for 1 ns with

[gmx-users] Regarding to relaxation time

 Hi Gromacs Friends , I have 4 molecule system in water Force field is G96 53a6 ..spc water molecule .. How to find out relaxation time of my system ??? All suggestion are welcome .. I saved trajectory after 0.2 ps .. Thank you in advance -- gmx-users mailing listgmx-users@gromacs.

Re: [gmx-users] em fatal error!

Hi Ankita , The error is self-explanatory , and simple to interpret it. You check the Topology file and see the last line that showing added ions ... What was your genion COMMAND LINE Have a nice day Rama On Mon, Apr 2, 2012 at 3:19 PM, Erik Marklund wrote

[gmx-users] Atom N not found....

Hi Gromacs friends, When I given the command ... pdb2gmx -f .. -o .. -p .. -ignh I gate the following error.. -- Program pdb2gmx, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pdb2top.c, line: 1070 Fatal error: atom N n

[gmx-users] Atom N not found....

the way to tackle these problem??? With Best Wishes, R.Davaid On Thu, Apr 5, 2012 at 4:13 PM, Justin A. Lemkul wrote: > > > rama david wrote: > >> Hi Gromacs friends, >> >> When I given the command ... >> pdb2gmx -f .. -o .. -p ..

Re: [gmx-users] Atom N not found....

at 4:38 PM, Mark Abraham wrote: > On 6/04/2012 9:05 PM, Mark Abraham wrote: > > On 6/04/2012 8:27 PM, rama david wrote: > > Hi Gromacs Friends and Justin , > > Thank you for reply and suggestion. > > These is short part of my PDB . > > ATOM 1 1H ACE 1

Re: [gmx-users] Atom N not found....

HI all , sorry for above incomplete information , I change CH3 of ACE residue of my pdb file to CA . Thank you in advance On Fri, Apr 6, 2012 at 5:34 PM, rama david wrote: > Hi GROMACS Friends and Mark.. > > Thank you for reply ... > My command line is > pdb2gmx -f pdb -o

Re: [gmx-users] Atom N not found....

Hi Justin , Thank you , You are right . Problem get solved by change in spacing in PDB file. have a nice day. With Best Wishes, R.David On Fri, Apr 6, 2012 at 6:36 PM, Justin A. Lemkul wrote: > > > rama david wrote: > >> HI all , >> sorry for above incomplete informati

Re: [gmx-users] regarding rmsd and gyrate

Hi priya , I am also have same problem... >From my limited experience .. To solve these problem it is a good way to make index file of particular group (or molecule ) and then measure there g_mindist, g_gyrate and g_hbond You can get gyrate and hbond value for them... Have a nice Day ... With

Re: [gmx-users] regarding micelle and its analysis

Hi Priya, Check these link ..May be helpfull to you , http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering >From my limited Experience , I suggest ,you should have to make the group of the molecule as per they forming micelle (As u get the 2-3 micelle ) ,make 2-3 group by make_ndx com

Re: [gmx-users] How to fit ligand in specific site in protein in simulation

Hi sai, you have to used docked structure to simulation . 1st convert the dock structure ,that you concider imptortant for your further study to pdb file (As you used autodock for docking ). Then perform MD on that structure. Have a nice day... On Thu, Apr 12, 2012 at 2:14 PM, sai nitin wrote:

Re: [gmx-users] regarding micelle and its analysis - index group

Hi priya http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx these link may be help to you i like to know how to calculate index groups for my micelles.. since i am having two micelles , one having 8molecules and another having 2molecules.. residue number for that 2molecule micelle i

Re: [gmx-users] How to fit ligand in specific site in protein in simulation

Hi Sai, you have to concider the protein and ligand strucure togather (Docked structure ), After these follow the link ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html ) With Best Wishes, Rama On Thu, Apr 12, 2012 at 5:13 PM, sai nitin wrote: >

Re: [gmx-users] regarding micelle index group

priya thiyagarajan wrote: > hello sir, > > Thanks a lot for your help.. i got my own index file for my micelles using > make_ndx.. > > Thanking you, > > Hi Priya, > Try g_spatial tools for micelle study, http://www.gromacs.org/Documentation/Gromacs_Utilities/g_spatial Check proparly that your

[gmx-users] Justin protein-ligand complex...

Hi Gromacs user , In justin tutorial protein-ligand complex.. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/08_MD.html the production md.mdp has following parameter for Pressure and Temperature coupling ; Temperature coupling is on tcoupl = V-rescale

Re: [gmx-users] Justin protein-ligand complex...

On Sat, Apr 14, 2012 at 6:12 PM, Justin A. Lemkul wrote: > > > >> Hi Justin, Thank you for reply.. >> >> >> >> My query is ..Why Pressure Coupling is off in production MD run ??? >> > > Pressure coupling is on, hence: > > pcoupl = Parrinello-Rahman > That means sentence ; Pressure

[gmx-users] Charm forcefield error..Atomtype CR not found ..

: Atomtype CR not found How to solve the error.. All suggestion are welcome.. Thank you in Advance... Have a good day.!!! With Best Wishes, Rama David. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.g

Re: [gmx-users] Charm forcefield error..Atomtype CR not found ..

, Apr 21, 2012 at 6:27 PM, Mark Abraham wrote: > On 21/04/2012 9:27 PM, rama david wrote: >> >> Hi Gromacs Friends, >> >> I wish to apply charmff 27 to my protein and ligand >> I proceed in following way .. >> >> 1. I separate the protein and ligand by g

Re: [gmx-users] Fwd: help

HI vineetha, On Sat, Apr 21, 2012 at 9:32 PM, vineetha mandlik wrote: > > > > > > Respected Sir/Madam > > I am new to gromacs and on giving the grompp command after genion command > I am getting the following error: > > > > Even after running the genion command and adding 4 Na+ ions before the >

[gmx-users] About hydrogen bond ..

, Please help me to know the best way to determine hydrogen bonds number in trajectory by Gromacs.. With Best Wishes, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support

[gmx-users] Justin-lipid tutorial...

c.itp file has following statement at the last .. #ifdef POSRES_LIPID #include "lipid_posre.itp" #endif where are these file located If these file are not present why we are not get the any error With best wishes, Rama David -- gmx-users mailing listgmx-us

[gmx-users] Justin-lipid tutorial..

) Rama david -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or se

[gmx-users] Re: Justin lipid-position restraine

On Tue, May 8, 2012 at 1:00 PM, rama david wrote: > Hi Gromacs user, > I am doing the justin tutorial on lipid posted on link.. > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html > > I am following the tutorial very carefully

[gmx-users] justin-lipid tutorial........

ors --- "Making merry out of nothing, like in refugee camp" (Gogol Bordello) Please give me some valuable suggestion Rama David... With Best Wishes, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listi

Re: [gmx-users] about trifloroehanol

Thank you Justin .. I will follow your Instructions .. With Best Wishes, R.David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't po

Re: [gmx-users] about trifloroehanol

Thank you justin.. I will try to adhere spacing -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to t

[gmx-users] about trifloroehanol

e topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I tried a lot ... Please give me some suggestion ... Thank you in Advance ... Rama David .

Re: [gmx-users] about trifloroehanol

rid from error .. Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the

Re: [gmx-users] about the frame selection

On Tue, May 15, 2012 at 11:59 AM, Anirban wrote: > > > > Thank you Anirban I proceed as you > mentioned... -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search befor

Re: [gmx-users] about the frame selection

Thank you ANIRBAN for your reply .. > I think its better to remove the periodicity when you are going to start a > fresh simulation with this protein. > Could you told me how to remove the periodicity ??? > > >> Thank you in advance ... > > > > -- gmx-users mailing listgmx-users@gromacs

[gmx-users] about the frame selection

. Should I used the extracted frame directly for further study or I need to remove the periodicity...?? 2 . to change the box size how to proceed ?? Should I delete the line manually and adjust the box size All suggestion are welcome ... Than you in advance rama david

[gmx-users] TFE Proper Dihedral types...

Hi Gromacs Friends .. I am using TFE (Trifluro Ethanol ) as a solvent for my simulation study.. I am using G96 53a6 ff After the genbox -cp .. -cs tef.pdb -o mix.pdb I count the no of solvent molecule , to update topology .. after Grompp I am facing following error grompp -f minim.mdp -c mix.pd

Re: [gmx-users] TFE Proper Dihedral types...

bio.biosci.uq.edu.au/atb/download.py?molid=1655> > > -Justin > > Thank you Justin .. I obtain the topology from given link.. 1. If you have some time , Could you tell me the way how to fix the missing parameter from ffbonded.itp ..??? With Best Wishes, Rama David -- gmx-users mai

Re: [gmx-users] nvt equilibration output

Hi Priya, My query is different than your problem .. I wondered Is you use position restrained in nvt...?? In position restrained protein comes togather or you remove position restraind ... Sorry for trouble you... With Best wishes, Rama David -- gmx-users mailing listgmx-users

[gmx-users] (no subject)

every 5 step togather with pair list.. Please give me valuable suggestion .. Thank you in advance .. With Best Wishes, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support

[gmx-users] Justin-lipid tutorials..

0.350 and 0.320 (Tutorial mention to 0.375 ) to add more water .. But in both time at nvt lipid layer get separated Please give me valuable suggestion .. Thank you in advance.. With Best wishes, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

Re: [gmx-users] Justin-lipid tutorials..

dimension ...If yes Then what the value of Lower Z and Upper Z Thank you in Advance.. With Best Wishes, Rama David.. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Justin-lipid tutorials..

upper Z .. How to find out these hydropbhic region co-ordinate... 2. From your reply , I Think Lower and upper Z is the co-ordinate value , and in between these Z-region no water molecule get added... With Best Wishes, Rama david -- gmx-users mailing listgmx-users

[gmx-users] Justin umbrella sampling tutorial......

Hi Gromacs Friends, I am performing justin tutorial for umbrella sampling .. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html I encounter with following problem while using the disatances.pl script 1. After command perl distances.pl I got following

Re: [gmx-users] RE: Justin umbrella sampling tutorial...... (rama david)

et solve!!! Thank you With Best Wishes, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe reques

Re: [gmx-users] Justin umbrella sampling tutorial......

velocity from pull *(step five)* ) 3 . If we are using the gen_vel = yes continuation= yes If continuation is yes, then why gen_vel is yes Please shade some light on meaning of continuation and gen_vel Thank you in advance With Best Wishes, Rama David

Re: [gmx-users] Regarding error.

ke pr.mdp as mention in tutorial With Best Wishes, Rama David > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don

Re: [gmx-users] Justin umbrella sampling tutorial......

you, if you shade some light on these Sorry for trouble Thank you in advance With best wishes, Rama David Thank you in advance With Best Wishes, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

Re: [gmx-users] Justin umbrella sampling tutorial......

we are using same mdp file in both condition means the npt equilibriation is as same as md production , Then why to do npt, just run production md with DPOSRES_B With my best Wishes , Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

Re: [gmx-users] Justin umbrella sampling tutorial......

are almost same in parameter .. (Where you mentioned in mdp for npt to do restraints on all proteins heavy atoms and for production md restraining only one chain ..) Please accept my apology if I unable to explain you my problem Thank you in advance ... With best wishes, Rama david -- gmx-

Re: [gmx-users] trjconv_snapshot

ry with help of trjcat -h to get snapshot of particular time use trjconv -dump use appropriate pbc option you are using -b 1 -e 1 means the snapshot at 10 ns So I think conf20.gro is snapshot at 20 ns so they may differ ... With Best Wishes, Rama David -- gmx-users mailing listgmx-use

Re: [gmx-users] trjconv_snapshot

not a full trajectory, it just a trajectory of second 10ns simulation) with traj20ns.xtc if you need 20 ns snapshot use -b 2 -e 2 With Best Wishes, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

Re: [gmx-users] Re: Justin umbrella sampling tutorial......

pt my apology if I interpret any wrong and if unable to explain you my query.. Thanks to Justin and Thomas for there valuable guidance I will be a very greatfull to you if you help me to solve my simple query.. Thank you in advance... With Best Wishes, Rama David. -- gmx-users mailing list

Re: [gmx-users] Re: Justin umbrella sampling tutorial......

y wrong and if unable to explain > you my query.. > > Thanks to Justin and Thomas for there valuable guidance > > I will be a very greatfull to you if you help me to solve my simple > query.. > > > Thank you in advance... > > > With Best Wishes, > Rama

Re: [gmx-users] Re: Justin umbrella sampling tutorial......

se alternative process is right or totally wrong..??? Please give me a valuable suggestion. Thank you in advance. With Best Wishes, Rama David. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.

Re: [gmx-users] Re: Justin umbrella sampling tutorial......

ddle configuration.. Thank you for explaination ... I have another query.. In npt equilibration can I use define = -DPOSRES (Position restrain all the protein along the chain B) and in production md define = -DPOSRES_B ( Position restrain for chain B only..) ??? If not What is appropriate reas

Re: [gmx-users] Re: Justin umbrella sampling tutorial......

longer than the equilibration, and > the results will likely turn out the same, when considering error > estimates. Sufficient sampling of any series of simulations should > converge. > > > -Justin > > With Best Wishes, Rama David. -- gmx-users mailing listgmx-users@gromacs.org ht

[gmx-users] umbrella windows...

choose total 28 windows instead of 23 ...So is it good or bad ??? Thank you in Advance... With Best Wishes, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] About extend the run,,

t file as input to -mdrun, My query is, There are two cpt file a) pre.cpt b) .cpt , So which one has to given as input??? All suggestion are welcome... With Best Wishes, Rama david -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please sea

Re: [gmx-users] About extend the run,,

Thank you Justin for quick reply On Sat, Jun 2, 2012 at 8:12 PM, Justin A. Lemkul wrote: > > > To perform these task I am using following command >> 1. grompp -f -t <.cpt> -c >> <.gro >> file(gro file from position restrained run )> -o new.tpr >> >> >> 2. tpbconv -s new.tpr -0 extend.tp

Re: [gmx-users] About extend the run,,

Thank You for Quick reply Justin... On Sat, Jun 2, 2012 at 8:58 PM, Justin A. Lemkul wrote: > > You'll get a mismatch in your files (checkpoint, trajectory, energy) in > terms of frame interval. You should not try to append to these files or > extend the run. Just run a new simulation from 2

[gmx-users] About g_enemat problem

-- Forwarded message -- From: rama david Date: Wed, Dec 26, 2012 at 9:55 PM Subject: About g_enemat problem To: gmx-users-ow...@gromacs.org Hi Gromacs friend. I simulated a system containing random peptide I found that as they start to interact they change there secondary

Re: [gmx-users] enough time for simulation

. With Best Wishes and Regards, Rama David. On Tue, Jan 8, 2013 at 12:55 PM, mohammad agha wrote: > Dear GROMACS Specialists, > > I have one system consists of many surfactant molecules that they create > several micelles. How should I know that time of simulation is enough or

[gmx-users] REMD general protocol ...

are possible to implement in my work flow. I will be very grateful to you for your help and suggestion. With Best Regards, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org

Re: [gmx-users] REMD general protocol ...

or need to change much Thank you With Best Regards.. On Tue, Apr 2, 2013 at 5:08 PM, Erik Marklund wrote: > > On 2 Apr 2013, at 13:30, Justin Lemkul wrote: > > > > > > > On 4/2/13 7:13 AM, rama david wrote: > >> Dear friends, > >>

Re: [gmx-users] REMD general protocol ...

:45 PM, massimo sandal wrote: > I would look on some paper which temperature ranges and conditions > (NPT/NVT) were used for systems of a similar size and with a similar aim. > > > 2013/4/2 rama david > > > Dear friends , > > Thank you justin and Mark for your suggesti

Re: [gmx-users] REMD general protocol ...

Thank you justin. I will do the same. On Tue, Apr 2, 2013 at 10:06 PM, Justin Lemkul wrote: > > > On 4/2/13 9:24 AM, rama david wrote: > >> Thank you Massimo sandal, Justin and mark , >> >> I also goes through the article and GMX archive. >> But I confu

[gmx-users] About Free energy surface .....g_sas

g_sham -h, I tried it, but not understand properly) I will be very grateful for your suggestion and help.. With Best Wishes, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org

Re: [gmx-users] REMD temperature spacing formula

Dear http://folding.bmc.uu.se/remd/ this may help you. With best regards On Thu, Apr 4, 2013 at 11:43 AM, Nikunj Maheshwari wrote: > Dear all, > > We are stuck at the last stage of running a successful REMD. > We have obtained average potential energy by fitting the energy values from > init

Re: [gmx-users] About Free energy surface .....g_sas

best Regards Rama david. On Thu, Apr 4, 2013 at 1:56 PM, Justin Lemkul wrote: > > > On 4/4/13 2:14 AM, rama david wrote: > >> Dear Friends, >>I simulated the 4 peptide in water box . >> As they come close to each other they start to from anti-pa

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