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

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-users@gromacs.org http

[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 send

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

On Tue, May 8, 2012 at 1:00 PM, rama david ramadavidgr...@gmail.com 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........

--- 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/listinfo/gmx-users

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

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

[gmx-users] about trifloroehanol

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 ... -- gmx

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 www

Re: [gmx-users] about the frame selection

On Tue, May 15, 2012 at 11:59 AM, Anirban reach.anirban.gh...@gmail.comwrote: 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

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.org

[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

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

/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 mailing listgmx-users@gromacs.org

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)

for 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..

to 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..

and 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)

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 requests to the list. Use the www

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.

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 requests to the list. Use the www

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

to 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......

if 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......

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-users mailing listgmx

Re: [gmx-users] trjconv_snapshot

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-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] trjconv_snapshot

is 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......

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 listgmx

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

query.. 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/Search before posting! Please don't post (un

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

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.org/Support/Mailing_Lists/Search before posting! Please don't post (un

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

.. 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 reason??? Thank you in advance... With Best Wishes, Rama David. -- gmx

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

, 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 http://lists.gromacs.org/mailman/listinfo/gmx-users

[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,,

run, users give .cpt 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

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 jalem...@vt.edu wrote: To perform these task I am using following command 1. grompp -f New mdp file just change in saving output -t .cpt -c .gro file(gro file from position restrained run ) -o

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 jalem...@vt.edu 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

[gmx-users] LINCS warnings

. But Truly I dont Want to change the arrangment (distance 0.5 nm), Please Help me to solve the above problem, 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 search the archive

Re: [gmx-users] LINCS warnings

in z direction, Such that separation in each layer is 0.4 , I arranged eight layer in Z direction(total 24 peptide 8 * 4=32 ), All things was right. Thank you in Advance With Best Wishes, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

Re: [gmx-users] LINCS warnings

reason ) last option : you have a single water molecule somewhere within the system that is isolated from the other water molecules. How to find such water molecule and solve the problem?? Thank you in Advance . With Best Wishes, Rama David -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] LINCS warnings

Hi Justin, thank you for quick reply. You are right I have practicle result, And I want to replicate them.. Thank you for your suggestion.. With Best Wishes, Rama David On Mon, Jun 11, 2012 at 3:58 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 6/11/12 6:23 AM, rama david wrote: Hi Mark

[gmx-users] simulated annealing mdp

310 310 323 300 310 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/Search before posting! Please don't post (un

[gmx-users] Press Equilibration

Hi Gromacs Friends, I did NPT for 100 ps with folowing parameter ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t

Re: [gmx-users] simulated annealing mdp

THANK YOU Justin, -- 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

[gmx-users] Re: Press Equilibration

On Tue, Jun 12, 2012 at 4:40 PM, rama david ramadavidgr...@gmail.comwrote: Hi Gromacs Friends, I did NPT for 100 ps with folowing parameter ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling

Re: [gmx-users] Press Equilibration

thank you for Quick reply -- 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

Re: [gmx-users] simulated annealing mdp

is restrained and the sidechain is free to move, So I think it may be help to achieve my goal. After these I also plan to use SA as production run, then compare the result with previous protocols. Please give valuable suggestion to improve my study protocol.. With Best Wishes, Rama David

Re: [gmx-users] simulated annealing mdp

Thank you for reply -- 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

[gmx-users] Lipid-protein simulation....

Hi Gromacs Friends, I completed Justin-Lipid Tutorial. I plan to simulate protein-lipid system to study protein-lipid interaction. My Query is like 1. I plan to use DPPC (128) lipid from Tieleman Website. I removed its periodicity as per tutorial instruction.. I found that I need the z box

[gmx-users] Re: Lipid-protein simulation....

On Tue, Jun 26, 2012 at 9:32 PM, rama david ramadavidgr...@gmail.com wrote: Hi Gromacs Friends,  I completed Justin-Lipid Tutorial. I plan to simulate protein-lipid system  to study protein-lipid interaction. My Query is like 1. I plan to use DPPC (128) lipid from Tieleman Website.  I

[gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

Hi Gromacs Friends,     I am doing Justin-lipid tutorialer http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html In these the npt.mdp has a parameter refcoord_scaling = com Why these parameter is introduced in NPT of lipid-protein simulation  and not use in Lysozyme in

Fwd: [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

Thank you Justin for your Explaination Please Would you me the Reason Why these parameter is present in Equilibration mdp and not in production run mdp file ( for both lysozyme and lipid simulation ) With Best Wishes and regardsRama -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Fwd: About Justin Lipid-protein simulation tutorial

simulation??? How to check these parameter affect my result sensitivity??? Please give me valuable guidance to solve my query.. With Best Wishes and regards, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] Fwd: Determine sec structure by MD

Hi Gromacs Friends,         I have the experimental result of change in Secondary structure of peptide from random coil to Beta sheet, as  the conc increases ( but  not know the Parallel or anti-parallel )                        I run Simulation of ( 30ns ) two peptide in random coil structure

[gmx-users] About lipid simulation npt.mdp

???) Please give me the valuable suggestion in these regard Thank you in advance. Have a nice Day. With best wishes and regards, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search

[gmx-users] About lipid simulation...

( Perpendicular press ) ??? ( Why to say P|| = -30 Pz = 1 , will give the teral tension of 20 mNm/m ???) Please give me the valuable suggestion in these regard Thank you in advance. Have a nice Day. With best wishes and regards, Rama David -- gmx-users mailing listgmx-users

Re: [gmx-users] genconf command

Dear cuong nguyen.. I think use following commands. Try editconf -rotate for rotaion angle along axis along these use -center co-ordinate if you want to place canter of box at particular position Try editconf -translate For translation along axis On Tue, Jul 17, 2012 at 2:07 PM, Mark

[gmx-users] Re: About lipid simulation...

in advance. Have a nice Day. With best wishes and regards, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] About Surface tension in lipid simulation.....

Hi Gromacs Friends, I completed the Justin Protein KALP - lipid tutorial ... I want to simulate the DPPC lipid bilayer membrane under Stress condition ( Lateral tension = 20 mNm/m).. For stress condition I made the following npt.mdp ; Temperature coupling is on tcoupl =

[gmx-users] Gromacs installation

and regards. Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe

Re: [gmx-users] Gromacs installation

thank you for immediate reply... Suppose, If I installed from Fedora software packages How to check that Gromacs installed in Parallel version and can performed REMD Thank you in Advance.. -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Gromacs installation

Thank you M.ark.. I got following reply.. Fatal error : mdrun -multi is not supported with thread library .Please compile gromacs with MPI support. I have to try to compile gromacs as per the webpage instructions... With best wishes and regards.. Rama David.. -- gmx-users mailing listgmx

[gmx-users] About system requirement to gromacs

Precision T 3500 )... With best Wishes and Regards... Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] About system requirement to gromacs

. -- So what is wrong??? With best wishes and regards Rama david -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] About system requirement to gromacs

and regards Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe

Re: [gmx-users] About system requirement to gromacs

output is it able to perform REMD or not ? Is the gromacs installation on my system is right for open-mpi With Best Wishes and regards Rama david -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed

[gmx-users] Gromacs configuration error....configure error : cannot compute sizeof ( off_t)...

Hi Gromacs Friends, I am trying to install gromacs 4.5.4 in parallel operating system fedora 17 I am using dell T 3500 precision , 6C. I downloaded openmppi-1.6 Command line to install ./configure --prefix=/usr/local make all install For fftw 3.3.2 installation command line was .

Re: [gmx-users] Gromacs configuration error....configure error : cannot compute sizeof ( off_t)...

file: No such file or directory I have a small experience in linux only, That why I may be missing or done something wrong??? So please tell me where is the problem Thank you in advane.. With Best wishes and regards, Rama david. -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] checkpoint file

on Gromacs 4.5.4 With best wishes and regards, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before

Re: [gmx-users] grommp warning

With best wishes and regards Rama David.. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post

Re: [gmx-users] grommp warning

Justin, Thank you for your reply, I check the manual but it is giving only small information.. I would be greatly thankfull to you if you shed some light on these option ... With best wishes and regards Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

Re: [gmx-users] grommp warning

.?? Is there any way to find out which option to use when How all the things going to affect the result I goes trough archive but not find satisfactory answer... I am looking for clear and simple explanation... Thank you in advance.. With Best wishes and regards Rama david -- gmx-users

Re: [gmx-users] grommp warning

-ordinates or something else) I get confused Please accept my apology for stupid question Please help to come out through the confusion. With best wishes and regards Rama david -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain

Re: [gmx-users] my VMD

...here md.gro through browse open the md.xtc then load it.. With best wishes aned regards.. Rama david On Wed, Aug 15, 2012 at 3:27 PM, Acoot Brett acootbr...@yahoo.com wrote: Dear All, I just installed a VMD. And then I load a gro file and a xtc file from a simulation. The bar in the VMD

Re: [gmx-users] my VMD

Sorry md.pdb/md.gro On Thu, Aug 16, 2012 at 11:34 AM, rama david ramadavidgr...@gmail.com wrote: Hi do the following .. open the trajectory in tthe molecule not as seperate molecule.. As example you havre md.gro and md.xtc files.. file == new molecule load files for md.pdb open

Re: [gmx-users] on tpbconv

Yes it will work .. Just at the time of mdrun add -cpi cpt ( prvious cpt file ) With best wishes and regards..!! On Sun, Sep 30, 2012 at 8:48 AM, Acoot Brett acootbr...@yahoo.com wrote: Dear All, for my original MD, based on mdp file the total time is 500 ps. After it finished, I have

Re: [gmx-users] Calculate Density with respect to time...

you in advance.. With best wishes and 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/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe

Re: [gmx-users] A snapshot at a particular time frame

Dear Ravi Use trjconv -dump ... ( time in ps) With Best wishes and regards Rama david. On Mon, Oct 1, 2012 at 11:15 AM, Ravi Kumar Venkatraman ravikumarvenkatra...@gmail.com wrote: Dear All, How to get a snapshot at a particular time frame from the MDS run. Thank

Re: [gmx-users] Density measurment

).. Please, would you tell me another way to solve these problem..?? Thank you in advance Have a nice day. Rama David On Tue, Oct 2, 2012 at 8:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/2/12 7:07 AM, rama david wrote: Hi Gromacs Users, I did simulation

Re: [gmx-users] Problem with the installation of Gromacs 4-5.5

Hi Deepak, Is the gromacs is in your path?? Please mention your operating system.. With best wishes and Regards, rama david On Thu, Oct 4, 2012 at 11:07 AM, Deepak Ojha alwaysinthem...@gmail.comwrote: Dear All I want to use Amber force field in Gromacs therefore I installed the latest

Re: [gmx-users] Interaction study for peptide-receptor..

Essential Dynamics ??? or Principle component analysis ??? Would you suggest me any general protocol for such work?? Thank you in Advance With Best Wishes and regards. Rama David On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/4/12 2:01 AM, rama david wrote: Hi

Re: [gmx-users] Interaction study for peptide-receptor..

should have same effect..Am I right or wrong?? If you have any other way please suggest it.. With best wishes and regards Rama david On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri francesco.ot...@gmail.comwrote: Hi, as far as I know, freezing just set velocities to 0 so you gain nothing

Re: [gmx-users] Interaction study for peptide-receptor..

idea. Is any other way to do the same thing.. With best wishes and regards Rama David On Thu, Oct 4, 2012 at 5:47 PM, francesco oteri francesco.ot...@gmail.comwrote: 2012/10/4 rama david ramadavidgr...@gmail.com Hi francesco, Thank you For reply. I did docking but the result are not so

Re: [gmx-users] Interaction study for peptide-receptor..

in advance Thank you for giving your valuable time and advice to me. With best wishes and regards, Rama david On Thu, Oct 4, 2012 at 6:11 PM, Thomas Evangelidis teva...@gmail.comwrote: I don't think AutoDock and Vina are suitable for peptide docking. I would first try the FlexPepDocking module

Re: [gmx-users] Interaction energy calculation..

Hi justin, I completed the simulation , Now I want to use the selected residues of protein and ligand. How to do it Would you explain me in detail?? With best wishes and regards, Rama david. On Fri, Oct 5, 2012 at 3:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/5/12 5:49 AM, rama david

Re: [gmx-users] Interaction energy calculation..

Hi justin, thank you for reply. With best wishes and regards Rama david. On Fri, Oct 5, 2012 at 4:07 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/5/12 6:15 AM, rama david wrote: Hi justin, I completed the simulation , Now I want to use the selected residues of protein and ligand

Re: [gmx-users] Interaction energy..

have to choose ?? What is Lamb-energy??? Is I did any mistake??? or I have to use any else command ?? Thank you in advance With best wishes and regards. Rama david. On Fri, Oct 5, 2012 at 7:54 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/5/12 10:16 AM, rama david wrote: Hi gromacs

Re: [gmx-users] Interaction energy..

Hi justin, Ok now I get I have to modify mdp parameter .. Thank you, With best wishes and regards, Rama david On Fri, Oct 5, 2012 at 9:47 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/5/12 11:46 AM, rama david wrote: Thank you for your Help. I did the following tc-groups tcoupl

Re: [gmx-users] Interaction energy..

you in advance. With best wishes and regards, Rama david On Fri, Oct 5, 2012 at 10:32 PM, rama david ramadavidgr...@gmail.comwrote: Hi justin, Ok now I get I have to modify mdp parameter .. Thank you, With best wishes and regards, Rama david On Fri, Oct 5, 2012 at 9:47 PM, Justin

Re: [gmx-users] Interaction energy..

reference temperature for free energy calculation ) Any suggestion on these topic, is helpful to me. Thank you in advance, With best wishes and regards, Rama david. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search

Re: [gmx-users] Interaction energy..

-matrix of 2 groups, 3 elements, over 50001 frames Segmentation fault (core dumped) why program not work ?? Is it bug??? or Am I doing any stupid mistake??? Thank you in advance .. With best wishes and regards, Rama david On Sat, Oct 6, 2012 at 3:40 PM, Justin Lemkul jalem...@vt.edu wrote

Re: [gmx-users] Interaction energy..

Segmentation fault (core dumped) What is the reason ??? thank you in advance. With best wishes and regards Rama david. On Sat, Oct 6, 2012 at 6:47 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/6/12 6:26 AM, rama david wrote: Hi justin, I tried as per your suggestion. command line

Re: [gmx-users] how to center the protein?

and regards Rama david On Mon, Oct 8, 2012 at 3:06 PM, Albert mailmd2...@gmail.com wrote: Dear: I am using the command: trjconv -f md.trr -s md.tpr -dump 54000 -o md.pdb -pbc mol trjconv -f md.pdb -s md.tpr -o fit.pdb -fit rot+rans to extract a frame of my md simulation and I found my

Re: [gmx-users] Interaction energy..

50001 frames Segmentation fault (core dumped) On Mon, Oct 8, 2012 at 3:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/8/12 5:40 AM, rama david wrote: Hi justin, As per your advice, g_enemat -f ener.edr -groups groups.dat -nocoul -nolj Opened ener.edr as single precision energy

Re: [gmx-users] Interaction energy..

fault (core dumped) Thank you in advance Rama david. Let me be a bit more specific again. I previously suggested there was a problem with the -lj flag activating more than one option in the code, so that is a potential problem. I suggested adding -nolj -coul to test this theory. Please use

Re: [gmx-users] Interaction study for peptide-receptor..

the interaction energy. As the MD need a lot of time , you can´t use it for the large library. I plan to do only 5 simulation. With best wishes and regards. Rama david On Wed, Oct 10, 2012 at 6:54 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/9/12 9:17 PM, Liu Shiyong wrote: Justin, Single

Re: [gmx-users] Martini FF for Sec structure changes...

Thank you for your reply, Are these Cg can be used in Gromacs. Thank you in advance. With best wishes and regards, Rama david On Wed, Oct 10, 2012 at 6:13 PM, XAvier Periole x.peri...@rug.nl wrote: Martini FF cannot model changes in secondary structure ... other CG FF can. You'll find

Re: [gmx-users] Martini FF for Sec structure changes...

Hi thank you Please told me the name of Freely available software on which these FF can be used .. Thank you in advance With best wishes and regards, Rama david On Wed, Oct 10, 2012 at 6:26 PM, XAvier Periole x.peri...@rug.nl wrote: Nope, but on other softwares. On Oct 10, 2012, at 2

[gmx-users] REMD queries

I just confused with these options. So please give me proper protocol. Thank you in advance. With best wishes and 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

[gmx-users] about tc_grps in mdp file...

Dear all, I am running a system with sol 40646 atom and ion, NA 629 CL 634. At the time of nvt and npt should i have to make different *tc_grps* for ion and sol or should be make one group Nonprotein ( these include sol + ion)..these is default. With Best wishes and regards, Rama david -- gmx

Re: [gmx-users] Multiple protein simulations in a box

Dear Rajeswari, May I ask you why you want to do the multiple protein simulation.?? Please mention the purpose clearly, otherwise it is hard to understand what you are doing and what you need???, With best wishes and Regards, Rama David On Fri, Nov 2, 2012 at 3:22 PM, Rajeswari

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