Re: [gmx-users] Simulation of Primed DNA

Hi all, As per Justin's suggestion , I have created a rtp entry for primed THY residue..which is like this .. [ DT5P ] [ atoms ] H5THO0.44220 1 O5'O-0.63180 2 C5'CT -0.00690 3 H5'1H10.07540 4 H5'2H1

[gmx-users] Simulation of Primed DNA-rtp entry and Terminal residue

it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: Register (Rossen Apostolov) > 2. Re: make a new bond in VERSION 4.5.4 (Justin A. Lemkul) > 3. Re: Questions about GB parameters (Justin A. Lemku

[gmx-users] want to remove H5T entry form HDB file / open terminal (P, O) for polymerization of i-motif

Hi Friends, could anyone please guide me to get rid of the 5' H atom in terminal DT nucleotide. These are my entries.. PDB : 5'DT ATOM 1 PDT A 1 -6.726 -4.074 -28.509 1.00 0.00 P ATOM 2 O5' DT A 1 -5.444 -3.882 -27.274 1.00 0.00 O1- ATOM

[gmx-users] grompp error for customized topology

With Regards, Gurpreet Singh - University of Dortmund Department of Chemistry Physical Chemistry I - Biophysical Chemistry Otto-Hahn Str. 6 D-44227 Dortmund Germany Office: C1-06 room 176 Phone: +49 231 755 3916 Fax: +49 231 755

[gmx-users] simulations using structureless surface

range corrections. I would like to know the possibilities of simulating such systems using gromacs. With Regards, Gurpreet Singh ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] simulations using structureless surface-2

potentials. With Regards, Gurpreet Singh - University of Dortmund Department of Chemistry Physical Chemistry I - Biophysical Chemistry Otto-Hahn Str. 6 D-44227 Dortmund Germany Office: C1-06 room 176 Phone: +49 231 755 3916 Fax: +49 231 755

[gmx-users] simulations using structureless surface-2

"simple" but I totally get lost as soon as I open nonbonded.c Is there any other place where it will be relatively easier to implement it? With Regards, Gurpreet Singh - University of Dortmund Department of Chemistry Physical C

RE: [gmx-users] problems with parallel mdrun

-users] problems with parallel mdrun Gurpreet Singh wrote: > Dear gmx users, > > I am using a current CVS version of Gromacs and using the newly introduced > options for simulations with walls. I am facing the following two > problems. You should send separate emails for each problem,

RE: [gmx-users] problems with parallel mdrun

ccur when nx is divisible by number of nodes I have updated and compiled the CVS version yesterday only. With Regards, Gurpreet Singh - University of Dortmund Department of Chemistry Physical Chemistry I - Biophysical Chemistry Otto-Hahn Str.

[gmx-users] RE: problems with parallel mdrun

extend it ? The other suggested approach doesn't work as grompp from Gromacs 3.3.1 does not recognize the wall options of mdp files and gives errors. so it seems that back compatibility will not be there specially when using new features in mdp files. With Regards Gurpreet

[gmx-users] opls bonded parameters

that the first column entries in rtb file is only used to map PDB atom types to opls atom types and is of no further use. Please let me know if I am wrong. With Regards, Gurpreet Singh - University of Dortmund Department of Chemistry Phy

[gmx-users] opls

Dear Users, I am trying to simulate a capped pentapeptide using OPLS force field. Pdb2gmx runs successfully , however grompp gives following warnings WARNING 1 [file "topol.top", line 632]:   No default Ryckaert-Bell. types, using zeroes WARNING 2 [file "topol.top", line 857]:   No def

[gmx-users] opls

Dear Users, I am trying to simulate a capped pentapeptide using OPLS force field. Pdb2gmx runs successfully , however grompp gives following warnings WARNING 1 [file "topol.top", line 632]:   No default Ryckaert-Bell. types, using zeroes WARNING 2 [file "topol.top", line 857]:   No def

[gmx-users] RE: opls

ffoplsaabon.itp, I could not find an entry in dihedral types for these dihedrals. Regards, Gurpreet Singh Check your topology file against ffoplsaa.rtp and ffoplsaabon.itp Yang Ye singh wrote: > > Dear Users, > > I am trying to simulate a capped pentapeptide using OPLS force field. &g

[gmx-users] warnings in compilation of mdrun innerloops

m. With Regards, Gurpreet Singh - University of Dortmund Department of Chemistry Physical Chemistry I - Biophysical Chemistry Otto-Hahn Str. 6 D-44227 Dortmund Germany Office: C1-06 room 176 Phon

[gmx-users] do_dssp

, Gurpreet Singh - University of Dortmund Department of Chemistry Physical Chemistry I - Biophysical Chemistry Otto-Hahn Str. 6 D-44227 Dortmund Germany Office: C1-06 room 176 Phone: +49 231 755 3916 Fax: +49 231 755 3901

[gmx-users] do_dssp

this is the case, Is there any other way to assign secondary structure to such a system? Regards, Gurpreet Singh On 12/21/06, singh <[EMAIL PROTECTED]> wrote: > > > > > > > > > Dear Gromacs users, > > > > I have simulated 12 peptide fragments i

[gmx-users] PBC in g_gyrate

calculating radius of gyration for such a system. Regards, Gurpreet Singh - University of Dortmund Department of Chemistry Physical Chemistry I - Biophysical Chemistry Otto-Hahn Str. 6 D-44227 Dortmund Germany Office: C1-06 room 176 Phone: +49

[gmx-users] using fortran for xtc files

[test] Error 1 Any help is appreciated. With Regards, Gurpreet Singh - University of Dortmund Department of Chemistry Physical Chemistry I - Biophysical Chemistry Otto-Hahn Str. 6 D-44227 Dortmund Germany Office: C1-06 room 176 Phone: +4

[gmx-users] ref_temp and gen_temp during simulated annealing

distribution gen_temp= 328.0 ; temperature for Maxwell distribution gen_seed= 173529;generate a random seed -- * - Thanks and regards Bipin Singh * * * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] Conatant pH simulation in GROMACS

Hi all, I want to know that, whether we I can do constant pH simulation in gromacs. Please provide some details regarding this. -- * - Thanks and regards Bipin Singh * * * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] g_covar to calculate correlation of motion

suggest me the alternative way or does anyone have the modified g_covar for GROMKACS-4.5.3. -- * - Thanks and regards Bipin Singh * * * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] g_covar to calculate correlation of motion

n Feb 21, 2011 8:05 AM, "bipin singh" wrote: > > Dear GMX users, > I want to calculate the correlated motion between atoms during the md > simulation > > for that purpose I am using g_covar(the one which is available under > http://www.gromacs.org/Downloads/User

Re: [gmx-users] g_covar to calculate correlation of motion

ELEU > MET > MEVAL > NAC > NH2 > PHE > PHEH > PHEU > PHL > PRO > SER > THR > TRP > TRPH > TRPU > TYR > TYRH > TYRU > VAL > > > Groetjes, > > Tsjerk > > On Mon, Feb 21, 2011 at 8:47 AM, bipin singh wrote: > > Hi, > >

[gmx-users] H-bond autocorrelation doubts

calculating the autocorrelation because it is giving same result whether you use 298K or 500K I have read the manual but I am not clear about these functions. -- * - Thanks and regards Bipin Singh * * * -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] H-bond autocorrelation doubts

of your simulation. that way, your ACF > should remain meaningful. > > best > > Andre > > On Mon, Feb 28, 2011 at 10:36 AM, bipin singh > wrote: > > > > Hello, > > > > I am usng g_hbond to calculate H bond auto correlation during the > simulation &g

Re: [gmx-users] H-bond autocorrelation doubts

NO, its giving same result no matter what temperature you provide using -temp option. On Mon, Feb 28, 2011 at 23:55, Erik Marklund wrote: > It computes the same acf, but the thermodynamic/kinetic calculations give > different results for different -temp, don't they? > > Eri

[gmx-users] Error during PUMED installation for GROMACS-4.5.3

Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_zpath.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/testderivatives.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/*.Po': No such file or directory -

[gmx-users] Regarding DCCM analysis with g_covar available in user contributed section

ve attached my xpm matrix file generated using g_covar. -- * - Thanks and regards Bipin Singh * * * <>-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Supp

[gmx-users] Regarding editconf

3)How gromacs assign vectors length?If not provided in the editconf command. 4)How gromacs place solvent inside the box(genbox) , I mean using which method and how gromacs determine the the number of solvent to be placed inside the box. --- *Regards,* Bipin Singh -- gmx-users ma

[gmx-users] Regarding the construction of Dynamics cross correlation map from covar.dat(from g_covar)

expecting the stepwise procedure to construct the correlation matrix and not the theory behind it as it already stated in the previous posts. -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] Regarding the construction of Dynamics cross correlation map from covar.dat(from g_covar)

Hello users, Although there was already much discussion had been done on the procedure to construct DCCM map from covar.dat(i.e. output from g_covar) but still I am not clear with the step wise procedure to calculate the correlation matrix from covarience matrix(covar.dat). 1) It is stated in the

[gmx-users] Which structure to be used during covariance analysis

to calculate covariance during the simulation(Production run) (i) Structure after energy minimization (ii)Structure after equilibration (iii)Original crystal structure -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

[gmx-users] Re: Which structure to be used during covariance analysis

; covariance analysis, > If we want to calculate covariance during the simulation(Production run) > > (i) Structure after energy minimization > (ii)Structure after equilibration > (iii)Original crystal structure > -- > ------- > *Regards,* > Bipin S

Re: [gmx-users] Re: Which structure to be used during covariance analysis

Thanks Sir for you help regarding the doubt On Tue, Mar 29, 2011 at 22:49, Tsjerk Wassenaar wrote: > Hi Bipin, > > That won't really matter. The reference is just for fitting. > > Cheers, > > Tsjerk > > On Mar 29, 2011 3:51 PM, "bipin singh" w

[gmx-users] Regarding g_enemat

get these terms in energy file. The energy file I am supplying is from a 100 ns md simulation. -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.o

Re: [gmx-users] Regarding g_enemat

the energy file. On Thu, Apr 14, 2011 at 00:36, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Hello, >> >> I am using g_enemat to calculate the energy matrix from the energy >> file(edr file) and I am supplying Protein as a group in -groups >&g

[gmx-users] running job parallel

rati Singh System Administrator Centre for Computational Materials Science(CCMS) Jawaharlal Nehru Centre for Advanced Scientific Research(JNCASR), Bangalore - 560 064 India. mob. : 08970898515 Phone : +91 80 2208 2944 + Ext. 26 & 28 Fax : +91 80 2208 2906 Email : bharati_si...@jnca

Re: [gmx-users] running job parallel

log. > > Have you configured GROMACS using --enable-mpi? > > Thanks, > Saikat > > On Tue, May 3, 2011 at 2:35 PM, Bharati Singh wrote: > >> Hi Team, >> >> I have LSF in my cluster ,I have installed gromacs-4.0.7 on Sampige. It is >> working fine as a

Re: [gmx-users] running job parallel

Mentioned method is working in another user's home directory on same machine, then I dont think the problem with linking. On Tue, May 3, 2011 at 3:34 PM, Mark Abraham wrote: > On 3/05/2011 7:37 PM, Bharati Singh wrote: > > Hi Team, > > Thanks for your reply. > > I

Re: [gmx-users] running job parallel

Hi Mark, Sorry for your inconvenience As you said some kind of (dynamic) linking problem, Is it possible to resolve it? Thanks & Regards, Bharati On Tue, May 3, 2011 at 6:59 PM, Mark Abraham wrote: > On 3/05/2011 8:19 PM, Bharati Singh wrote: > > Mentioned method is worki

Re: [gmx-users] running job parallel

TH} > > > You are welcome, > > > -- > Best Regards, > > lina > -- > 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

Re: [gmx-users] running job parallel

Thank you Mark, for your valuable suggestion. Regards, Bharati On Wed, May 4, 2011 at 10:18 AM, Mark Abraham wrote: > > > On 04/05/11, *Bharati Singh * wrote: > > Hi Mark, > > Sorry for your inconvenience > As you said some kind of (dynamic) linking problem, Is it

[gmx-users] How to get angle distribution between two tyrosine stacking residues

Hello users, Can anyone tell how to calculate the normal-normal angle between two stacking tyrosine residues as a function of time. -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] compilation of g_hbond after bugfix

filed with donor and >acceptor swapped. */ > } >Simple as that -- --- Thanks & Regards, Bipin Singh -- 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/Maili

[gmx-users] Error in energy group exclusion

, Bipin Singh -- 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

Re: [gmx-users] Error in energy group exclusion

.. On Mon, May 23, 2011 at 21:28, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Hello users, >> I am getting the following warning during the grompp >> >> - >> WAR

Re: [gmx-users] Error in energy group exclusion

Mon, May 23, 2011 at 23:06, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Thanks for your reply, >> I have already done with the final simulation, and now if I have to >> change the method for electrostatic calculation(instead of PME) >> for energy g

[gmx-users] Regarding calculation of Salt bridge between specific group of atoms

, while g_mindist gives us the minimum distance between any pair of atom. My doubt is that which distance(either given by g_dist or g_mindist) corresponds to the salt bridge interaction distance between two atoms. -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users

Re: [gmx-users] Regarding calculation of Salt bridge between specific group of atoms

Thanks Sir, I understood.. On Sat, Jun 11, 2011 at 17:30, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Dear all, >> >> I want to calculate the salt bridge interaction between a particular >> set of residues, >> because I can not use

[gmx-users] Regarding H-bond autocorrelation

.. -- --- Thanks and Regards, Bipin Singh -- 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

[gmx-users] Regarding H-bond autocorrelation

.. -- --- Thanks and Regards, Bipin Singh -- --- Regards, Bipin Singh -- 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

Re: [gmx-users] Regarding H-bond autocorrelation

feature had been taken away, > however. Are you using old code? > > Erik > > 12 jun 2011 kl. 19.33 skrev bipin singh: > >> Hello, >> >> I am calculating the H-bond autocorrelation using g_hbond for my >> system, but after plotting >> I have observed t

Re: [gmx-users] Regarding H-bond autocorrelation

erves me right, there's another dataset in the > output, which shows the acf without the "background subtraction". > > Erik > > 14 jun 2011 kl. 12.10 skrev bipin singh: > >> I am using the Gromacs 4.5.3is  that feature is present in >> this ve

[gmx-users] Regarding H-bond autocorrelation

erves me right, there's another dataset in the > output, which shows the acf without the "background subtraction". > > Erik > > 14 jun 2011 kl. 12.10 skrev bipin singh: > >> I am using the Gromacs 4.5.3is  that feature is present in >> this ve

Re: [gmx-users] cross correlations

gt; >> * Zernike Institute for Advanced Materials > >> University of Groningen > >> The Netherlands > > > > -- > > Best Regards, > > Alexey 'Alexxy' Shvetsov > > Petersburg Nuclear Physics Institute, Russia > > Depar

[gmx-users] Regarding g_dist -dist option

Hello, I just want to ask that in g_dist module, -dist option expect distance as a real argument, so the distance should be in nm or A for that... -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

Re: [gmx-users] Regarding g_dist -dist option

Thanks... On Fri, Jun 24, 2011 at 20:17, shivangi nangia wrote: > > > On Fri, Jun 24, 2011 at 10:45 AM, bipin singh wrote: > >> Hello, >> I just want to ask that in g_dist module, -dist option expect distance as >> a real argument, so the distance

Re: [gmx-users] cross correlations

; > On Jun 24, 2011 3:28 PM, "bipin singh" wrote: > > Hello, > I have some doubts regarding the output file correl.dat as it contains 3 > columns, but I am not able to get what are > these column contains,I mean how to change it to the format in which I can > directly plot

Re: [gmx-users] cross correlations

wrote: > Hi Bipin, > > Read them in as a vector of numbers and divide them into sqrt(len(vector)) > rows to get yourself a nice square correlation matrix. > > Cheers, > > Tsjerk > > On Jun 24, 2011 3:28 PM, "bipin singh" wrote: > > Hello, > I have so

[gmx-users] Simulation of Primed DNA

Dear Experts, Hi from a beginner in Gromacs, I am trying to simulate i-motif so I have primed all the four chains and manually created a phosphodiester bond between two i-motif units. all the with Amber/Gromos ff the problem is : Fatal error: Atom P in residue DT 1 was not found in rtp entry DT

[gmx-users] Energy Calculation

Dear GMX user, I want to calculate the bonding energy between between two specific atoms. If it is possible, please help me. Cheers, Dhana -- 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] Regarding DispCorr

Hello, Please let me know, Whether it is correct to use DispCorr=EnerPres during energy minimization. -- --- Thanks and Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] Regarding DispCorr

On 19/02/2012 11:21 PM, bipin singh wrote: >> >> Hello, >> >> Please let me know, Whether it is correct to use DispCorr=EnerPres >> during energy minimization. >> > > What does it do? > > Mark > -- > gmx-users mailing list    gmx-users@gromacs.org

Re: [gmx-users] Regarding DispCorr

Thank you so much Sir for clearing my doubts. I understood your point. On Mon, Feb 20, 2012 at 12:51, Mark Abraham wrote: > On 20/02/2012 4:19 PM, bipin singh wrote: > >> Thanks for your help. But I am getting different results for potential >> energy when minimization done

Re: [gmx-users] Simulated Annealing Protocol...

odel the behavior of your system in response to a > change in termperature, then SA is your production run and you would not use > position restraints. > > It is still not clear to me how you wish to use SA or what you hope to > observe from it, so that's the best I can offer. &

[gmx-users] How to add dihedral information from the GAFF topology

? -- --- Thanks and Regards, Bipin Singh -- 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

Re: [gmx-users] Re: How to add dihedral information from the GAFF topology

]: No default Proper Dih. types Please provide your suggestions. On Mon, Mar 26, 2012 at 17:29, David van der Spoel wrote: > On 2012-03-26 13:55, bipin singh wrote: >> >> Hello all, >> >> I am using the GAFF topology provided for octan-1-ol at Groma

Re: [gmx-users] Re: How to add dihedral information from the GAFF topology

On Mon, Mar 26, 2012 at 18:46, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Thanks for your reply. >> But as far as I understood, in order to use these GAFF topology (for >> e.g. to perform simulation using these topologies) with Gromacs we >> have to

Re: [gmx-users] Re: How to add dihedral information from the GAFF topology

#mols Protein_chain_A 1 Ion_chain_A21 1-octanol 1 SOL 565 SOL 8495 # --- Please provide your comments. On Tue, Mar 27, 2012 at 03:20, Justin A. Lemkul wrote: > > > bipin singh wro

Re: [gmx-users] Re: How to add dihedral information from the GAFF topology

565 1-octanol 1 SOL 8422 Please provide suggestions. On Tue, Mar 27, 2012 at 17:59, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Thanks for your inputs. >> I have followed your suggestion and included the .itp for the oc

Re: [gmx-users] Re: How to add dihedral information from the GAFF topology

mx-users mailing list    gmx-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 it to gmx-users-req

Re: [gmx-users] Re: How to add dihedral information from the GAFF topology

A lot of thanks to your "charitable mood" now the things has been resolved :) . Thanks again. On Wed, Mar 28, 2012 at 18:24, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Thanks again >> > > For the record, I didn't ask that you send

[gmx-users] Pressure coupling doubt

compressibility= 4.5e-5 does it will affect the NVT criteria ? or It will ignore the compressibility input? -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] Pressure coupling and Isothermal compressibility for a biphasic system

water and octane have different compressibility, is it possible to mention the compressibility of water and octane separately? Please provide your suggestions. -- --- Thanks and Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

[gmx-users] Different results from identical tpr after MD

Bipin Singh -- 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

Re: [gmx-users] Different results from identical tpr after MD

/RNA) itself for a short simulation, where we don't have enough resources to run infinitely long simulation. And also how to believe the statement made by several research papers based on unconverged simulations. On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul wrote: > > > bipin singh

Re: [gmx-users] Different results from identical tpr after MD

. On Thu, Apr 5, 2012 at 23:50, Peter C. Lai wrote: > Well you're really supposed to conduct multiple runs anyway. > Remember, a single MD run over a period of time only samples 1 possible > trajectory out of the ensemble of possible trajectories... > > On 2012-04-05 11:38:20P

Re: [gmx-users] Different results from identical tpr after MD

Thanks for your valuable suggestions. I am totally agree with your views. On Fri, Apr 6, 2012 at 00:11, Justin A. Lemkul wrote: > > > bipin singh wrote: > >> Thanks for the reply. >> / /I read the link. So, how one can predict something reliable using >> these re

Re: [gmx-users] MD after equilibration phase

x-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 it to gmx-users-requ..

Re: [gmx-users] MD after equilibration phase

kul wrote: > > > bipin singh wrote: > >> Also, if we give continuation=yes in mdp file and use input as pdb file >> as input instead of gro file, grompp never complainsI don't no how it >> reads velocities from pdb file (as no velocities are present in pdb

Re: [gmx-users] MD after equilibration phase

Thanks for your comments. One more question. Does Gromacs saves velocities in pdb files, when we use gen_vel=yes option in mdp and save the output(-c) of mdrun as pdb file instead of gro file. On Fri, Apr 6, 2012 at 19:48, Mark Abraham wrote: > On 7/04/2012 12:15 AM, bipin singh wr

Re: [gmx-users] MD after equilibration phase

:2 and will the results got from the RUN:1 is unreliable ? If yes why ? On Fri, Apr 6, 2012 at 20:26, Mark Abraham wrote: > On 7/04/2012 12:37 AM, Justin A. Lemkul wrote: > >> >> >> bipin singh wrote: >> >>> Thanks for your comments. >>> One mor

[gmx-users] Regarding g_sham

). -- --- Thanks and Regards, Bipin Singh -- 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)subs

[gmx-users] Electric field GROMACS

Dear GROMACS users, A couple of days back I posted an issue which I have been facing, I request you all to kindly help me.. I posted the following issue: I ran a simulation using E_x as 1, 0.002, 0 i.e. i wanted a 0.002 V/nm electric field strength. The simulation completed successfully. But now

[gmx-users] Regarding manual velocity generation in simulation

Hello All, Please let me know whether is it possible to manually assign the velocity for each atom in the simulation instead of generating through gen_vel option. -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Reference structure for PCA.

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 sen

[gmx-users] MDP settings for No Temperature Coupling

tc_grps= group1 group2 ref_t= 300 10 gen_vel= yes gen_temp= 10 -- *--- Thanks and Regards, Bipin Singh* -- 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] Difference in Number of contacts through g_hbond and g_mindist

. -- *--- Thanks and Regards, Bipin Singh* -- 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

Re: [gmx-users] Difference in Number of contacts through g_hbond and g_mindist

Thanks for the reply. The difference is almost double, through g_hbond the average number of contacts are 1821 and through g_mindist it is 3643. The calculation group does not contains hydrogen atoms. On Mon, Mar 4, 2013 at 8:14 PM, Justin Lemkul wrote: > > > On 3/4/13 9:08 AM, bi

Re: [gmx-users] Difference in Number of contacts through g_hbond and g_mindist

Thanks a lot for the suggestions. It worked. On Mon, Mar 4, 2013 at 8:44 PM, Erik Marklund wrote: > As Justin implied, -merge could potentially make a factor of 2. Try > g_hbond -nomerge. > > Erik > > > On Mar 4, 2013, at 4:02 PM, bipin singh wrote: > > Thanks for t

[gmx-users] constant velocity pulling/Umbrella sampling

Hello Fellow Users, I have a doubt about the mdp option in case of constant velocity pulling / Umbrella pulling simulation. pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N N Y pull_start = yes ; define initial COM distance >

[gmx-users] pull code - constraint pulling - forces are zeros

Hello Fellow Users, I am trying to pull a DNA molecule. I have fixed one end and trying to pull the other one using this .mdp file.. force output is all zeros. I have tried going through the user-list but have not found any solution yet. I am using gmx-version 4.5.5. Any idea why is it happening.

[gmx-users] SMD : pulling both primes of DNA

Hello All, My simulation system is composed of DNA and want to pull both of the primes at the same time towards each other. I have tried every possible set of parameters in pull code...and i am not able to pull them together. it's like ... the DNA molecule is aligned along Y-axis and if want to p

Re: [gmx-users] Free energy landscape by g_sham

; www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- --- Thanks and Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-u

Re: [gmx-users] Re: Salt bridge Calculations

Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- --- Thanks an

[gmx-users] -vsite in Umbrella sampling

Hello Fellow Users, I have a question regarding US simulation. I am interested to know that can I treat hydrogens as virtual sites in US simulations?? I have very large protein complexes and to use higher time stepping during simulations...I am thinking to use -vsite option. what do you guys sugg

[gmx-users] Simulations box type

Hello All, I am here not with a problem but still i need your suggestions. I have a linear DNA molecule of 200nm in length and want to rum MD to calculate some bending properties. I want to know ...what kind of solvation box type will be good for such molecule?? Thank you cheers Raghav -- gmx-

[gmx-users] RMSD from the average structure

Singh* -- 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] Doubt about the Gromacs versions

Hi, Please let me know which one is the recent version of gromacs (with latest bugfixes) among the below. 4.5.7 and 4.6.1 And what is the reason behind the update for 4.5.x versions if 4.6.x versions are already available. -- *--- Thanks and Regards, Bipin Singh* -- gmx

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