[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

_contributions/Other_software) > > > but it is not compatible with the GROMACS-4.5.3, so please suggest me the > alternative way or does anyone have the modified g_covar for > GROMKACS-4.5.3. > > -- > * > - > Thanks and regards

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] 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] 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

converted both the input tpr to mdp using gmxdump and diff the two files and found that the mdp is identical. Please let me know what can be the reason of this behaviour. I know that it is unexpected and even I can't believe how can it be possible. -- --- *Thanks and Regards,*

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] 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

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] RMSD from the average structure

Hi all, Please let me know whether this is the right way to calculate RMSD from the average structure from a simulation: g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg average.pdb: is the pdb file produced using -ox option of g_rmsf. -- *--- Thanks and Regards, Bipin

[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

Re: [gmx-users] RMSD from the average structure

in real solution phase, a system may not be static and if we consider the time average structure of a simulation to be the real representative of the structure in solution phase rather than static crystal structure. On Fri, Apr 26, 2013 at 2:06 AM, Tsjerk Wassenaar wrote: > Hi Bipin Si

Re: [gmx-users] Doubt about the Gromacs versions

rg/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subs

Re: [gmx-users] Doubt about the Gromacs versions

ster). This series will also probably receive more attention in terms of > bug fixes and new releases (though I'm not a developer so I could be wrong > about that). > > Richard > > > > On 25/04/13 14:39, bipin singh wrote: > >> Hi, >> >> Please let me

Re: [gmx-users] RMSD from the average structure

nd causes the average positions of the > hydrogens to line up. Consider using g_cluster to find representative > structures from your trajectory. > > Erik > > On 26 Apr 2013, at 06:59, bipin singh wrote: > > > Thanks for your reply. > > Actually I am interest

[gmx-users] Temperature for individual amino acid residues

the constraints. Please let me know what type of correction need to done on the output from g_traj if we need correct temperature values. OR Is there any way to get it from .edr file... -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Temperature for individual amino acid residues

ue in a protein ? On Thu, May 2, 2013 at 4:56 PM, Justin Lemkul wrote: > > > On 5/2/13 1:54 AM, bipin singh wrote: > >> Hi All, >> >> I want to calculate temperature for each individual amino acids residues >> present in a protein after the simulation. I know

Re: [gmx-users] Temperature for individual amino acid residues

Thanks for your reply and suggestions. On Thu, May 2, 2013 at 8:09 PM, Justin Lemkul wrote: > > > On 5/2/13 10:28 AM, bipin singh wrote: > >> Thanks for the reply. >> I have seen the link. As given in the link that we need to multiply the >> temperature by (3N-Nc

[gmx-users] Regarding Pulling simulation:To study the base flipping of the thymine

Hi all, I am studying a system which consists of DNA duplex 20 base pairs. Actually I am interested in studying the base flipping of the thymine. I have the crystal structure of extrahelical DNA in which thymine is out side the helical structure. I want use pulling simulations to bring this base

[gmx-users] Segmentation fault while calculating water mediated H-bond with g_hbond

provide your suggestions to rectify the error. -- --- *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

[gmx-users] Angle between two six membered rings

me the correct way to calculate it in gromacs . -- --- 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

[gmx-users] fraction of native contacts calculation

Hello all, Is there any way to calculate fraction of native contacts during the simulation in gromacs. I searched the archives but didn't found any significant clue. *-- --- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] fraction of native contacts calculation

13.43 skrev Justin Lemkul: > > > > > > > On 10/31/12 6:02 AM, bipin singh wrote: > >> Hello all, > >> > >> Is there any way to calculate fraction of native contacts during the > >> simulation in gromacs. I searched the archives but didn't

Re: [gmx-users] fraction of native contacts calculation

Thanks for the information. On Thu, Nov 1, 2012 at 10:56 PM, Justin Lemkul wrote: > > > On 11/1/12 1:23 PM, bipin singh wrote: > >> Thanks for your response. Hope to see this feature in upcoming GROMACS >> release. Before that, could it be possible to get the modi

Re: [gmx-users] fraction of native contacts calculation

se 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...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing

Re: [gmx-users] fraction of native contacts calculation

ong with the native .gro file in VMD and > use Plumed plugin inbuilt in VMD . You need to install plumed most probably > early. > > > > ____ > From: bipin singh > To: Discussion list for GROMACS users > Sent: Thursday, November 1, 2012 1:23 PM

[gmx-users] Essential dynamics (ED) sampling using make_edi

-tau -alpha -T *3) *Will the output trajectory (produced using mdrun -ei sam.edi ) contain all atoms or only the C-alpha atoms (using the above make_edi command). -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] which chain to select for MD simulation

results. -- --- *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 req

Re: [gmx-users] which chain to select for MD simulation

mark.abra...@anu.edu.au > Fecha: 08-jul-2011 3:44 > Para: "Discussion list for GROMACS users" > Asunto: Re: [gmx-users] which chain to select for MD simulation > > > On 8/07/2011 4:52 PM, bipin singh wrote: > > Hello, > > > > My protein have two identical

[gmx-users] Concatenating two trajectories

below commands is right for concatenating these two trajectories: trjcat -f 1.xtc 2.xtc -o concat.xtc -cat -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

Re: [gmx-users] Concatenating two trajectories

Yes It is workingbut I have not tried that, what would be the difference if I don't give -cat option On Wed, Jul 20, 2011 at 16:16, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Hello, >> >> I want concatenate two trajectories which

Re: [gmx-users] Concatenating two trajectories

Thanks Sir, I understood... On Wed, Jul 20, 2011 at 16:46, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Yes It is workingbut I have not tried that, what would be the >> difference if I don't give -cat option >> > > If the times ar

[gmx-users] Regarding PCA and FEL

Hello, I have constructed free energy landscape(g_sham) based on the first two principal components, can anyone suggest how to find the representative conformation for a particular region on this 2-d landscape. -- --- Regards, Bipin Singh -- gmx-users mailing listgmx

[gmx-users] Regarding PCA and Free energy landscape

Hello, I have constructed free energy landscape(g_sham) based on the first two principal components, can anyone suggest how to find the representative conformation for a particular region on this 2-d landscape. -- --- Regards, Bipin Singh -- gmx-users mailing listgmx

[gmx-users] Regarding PCA and Gibbs Free energy landscape

landscape I want to map the conformation(structures from the MD trajectories) of the protein onto the different region(for eg:minima)of this landscape. Please suggest how can I perform this task. -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] PCA and Free energy landscape

landscape I want to map the conformations(structures from the MD trajectories) of the protein onto the different region(for eg:minima)of this landscape. Please suggest how can I perform this task -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users

[gmx-users] Regarding g_sham

-- --- 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 list. Use the

[gmx-users] Regarding g_sham

-- --- 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 list. Use the www inte

Re: [gmx-users] Regarding g_sham

Thanks for yor reply... I have read manual but there is no description available for the -map -ls3 -mdata options of g_sham On Sat, Aug 13, 2011 at 15:56, lina wrote: > On Sat, Aug 13, 2011 at 3:36 PM, bipin singh wrote: >> Hello, >> Please let me know from where can I get the f

[gmx-users] Regarding g_sham:Please reply

-- --- 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 list. Use the www inte

[gmx-users] Regarding xpm2ps

and y-axis range from -4 to +4. -- --- 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

Re: [gmx-users] Regarding xpm2ps

-font = Helvetica y-tickfontsize = 8 y-tickfont = Helvetica On Wed, Aug 24, 2011 at 00:52, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Hello, >> >> I have xpm matrix file, for converting this file to ps format I am using >> xpm2ps >> e.g

Re: [gmx-users] Regarding xpm2ps

from -4 to +4(PC1) and y-axis range from -5 to +4(PC2) regardless of the data values in xpm file. But I am unable to get using .m2p file. On Wed, Aug 24, 2011 at 16:22, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Hello, >> I am using the below .m2p file as inp

Re: [gmx-users] Regarding xpm2ps

Thanks for your kind help, I have tried as per your suggestion, the below command g_sham -f 2d_proj.xvg -xmin -5 -xmax 5 -ls gibbs.xpm It is running without any error , but it is not giving any xpm output... On Wed, Aug 24, 2011 at 17:18, Justin A. Lemkul wrote: > > > bipin si

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