[gmx-users] Charges in vacuum simulation

Hi all, I'm trying to run a vacuum simulation of my protein which has a non-zero charge. How to deal with this charge? Can I add counter ions in to my system? Would it be energetically stable? How can one bring a protein to its isoelectric point? -- gmx-users mailing listgmx-users@gromacs.or

Re: [gmx-users] a new GROMACS simulation tool

Hi Kevin I would like to try it out.. Let me know the procedure to create an account.. Regards Ash On Tuesday, October 22, 2013, Kevin Chen wrote: > Hi Everyone, > > I'm writing to let you guys know that we have developed a web-based tool MD > simulation tool for GROMACS. It is a software pack

Re: [gmx-users] Number of ligand contacts over the trajectories

; * 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-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Calculating the distance between protein and ligand during ligand diffusion out of the box

your protein and what you're doing but you > should consider if it's even relevant whether the ligand is 2nm away or 5? > > -Trayder > > > > On Tue, Oct 8, 2013 at 6:53 AM, Justin Lemkul wrote: > > > > > > > On 10/7/13 1:39 PM, bipin singh wrote: >

Re: [gmx-users] Calculating the distance between protein and ligand during ligand diffusion out of the box

a feasible behaviour during a simulation. http://researchweb.iiit.ac.in/~bipin.singh/plot.png On Mon, Oct 7, 2013 at 8:22 PM, Justin Lemkul wrote: > > > On 10/7/13 10:46 AM, bipin singh wrote: > >> Hello All, >> >> I have calculated the distance between the bindin

[gmx-users] Calculating the distance between protein and ligand during ligand diffusion out of the box

fitted my trajectory with using trjconv -pbc mol -ur compact -center (protein) option. I have also tried the -nojump option but getting the same results for distances. Please suggest how to get the real distance without the PBC effect. -- *--- Thanks and Regards, Bipin Singh

[gmx-users] Regarding atom numbering in .top and .gro files

. -- *--- 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 t

Re: [gmx-users] Regarding gromos method in g_cluster

> Tsjerk > > > On Wed, Jul 31, 2013 at 9:45 AM, bipin singh wrote: > > > Thanks for the reply Prof. David. But in the output it shows that "The > RMSD > > ranges from 0.0602553 to 0.411066 nm"; this is the point of confusion to > > me. So I think it

Re: [gmx-users] Regarding gromos method in g_cluster

PM, David van der Spoel wrote: > On 2013-07-31 07:20, bipin singh wrote: > >> Hello All, >> >> I was trying to do clustering on my MD trajectory using gromos method >> under >> g_cluster module. I got one doubt regarding the output, as I used the >> cutoff

[gmx-users] Regarding gromos method in g_cluster

## -- *--- 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

Re: [gmx-users] Getting a .tpr file for C-alpha atoms from an all atom .tpr file

Thanks a lot. On Tue, Jul 23, 2013 at 9:37 PM, Justin Lemkul wrote: > > > On 7/23/13 11:58 AM, bipin singh wrote: > >> Hello All, >> >> I there any way to get a .tpr for C-alpha atoms from an all atom .tpr >> file. >> >>

[gmx-users] Getting a .tpr file for C-alpha atoms from an all atom .tpr file

Hello All, I there any way to get a .tpr for C-alpha atoms from an all atom .tpr file. -- *--- 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

Re: [gmx-users] g_hbond for trajectory without having box information

two, there is random difference of 1-3 H-bonds at some point of time. On Fri, Jul 19, 2013 at 2:43 PM, Justin Lemkul wrote: > > > On 7/19/13 4:17 AM, bipin singh wrote: > >> According to the suggestion I added the box to the trajectory using -box >> option of trjc

Re: [gmx-users] g_hbond for trajectory without having box information

singh wrote: > Thanks a lot Prof. David. I will try this. > > > On Fri, Jul 19, 2013 at 10:45 AM, David van der Spoel < > sp...@xray.bmc.uu.se> wrote: > >> On 2013-07-19 06:26, bipin singh wrote: >> >>> Hello all, >>> >>> I was using g_hb

Re: [gmx-users] g_hbond for trajectory without having box information

Thanks a lot Prof. David. I will try this. On Fri, Jul 19, 2013 at 10:45 AM, David van der Spoel wrote: > On 2013-07-19 06:26, bipin singh wrote: > >> Hello all, >> >> I was using g_hbond to calculate H-bonds for a trajectory made from >> several >> individu

[gmx-users] g_hbond for trajectory without having box information

shrunk too much. g_hbond_mpi can not handle this situation, sorry. Please let me know, if there is any way to rectify this error. -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] Testing the performance of

Thanks! Mark. I got solution to my problem. For my system, setting pinoffset = 0, 16 and pinstride = 1 for two simultaneous simulations gave much satisfactory performance both for Verlet and Group cutoff-scheme. I tried it for 4 simultaneous simulations also with pinoffset = 0, 8, 16, 24 and pinst

Re: [gmx-users] TRACE OF RMSD COMPARISON MATRIX

romacsWrapper/gromacs/core/fileformats/xpm.html >> >> -g >> -- >> Gaurav Goel >> Assistant Professor >> Department of Chemical Engineering >> Indian Institute of Technology, Delhi >> Hauz Khas, New Delhi 110016 >> India >> >> On 02-Ju

[gmx-users] Testing the performance of

Hello, I want some inputs on observed performance of protein-in-water simulations run on a single server with 2 Intel Xeon E5-2660 processors. Each processor has 8C/16T, so total 16C/32T. My system is composed of 1643 beta-microglobulin atoms and 24699 water atoms. I ran several 500ps simulation

[gmx-users] TRACE OF RMSD COMPARISON MATRIX

Hello users, I'm using g_rms to compare my actual trajectory obtained from simulation with the filtered trajectory (along given set of eigenvectors), this gives me an RMSD comparison matrix in xpm format where the values of the plot are not clear. Is there any way which can help me to get the valu

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

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

[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] 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

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] Doubt about the Gromacs versions

cribe 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<http://www.gromacs.org/Support/Mailing_Lists> > -- *--- Thanks and Regards, Bipin Singh*

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

[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

[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] 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] -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

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

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

[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

[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] 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 >

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] 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

[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

[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

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] 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

[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] 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

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

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

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

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

[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

[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] 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] Gromacs-CPMD ....versions???

Hello Fellow Users, I wanted to know about the gromacs versions compatible with interfacing ...with CPMD QM/MM...??? is that particular version provided by Dr. Biswas is the only one or the latest versions are also capable of doing so??? Any News or info..or way??? Thank you all cheers Raghav

[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] 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

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

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

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

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] 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] 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

/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

[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

[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] 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

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

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

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

#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

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

]: 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

[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] 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. &

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] 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

[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

[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

Re: [gmx-users] Regarding free energy calculation

news is that if you move away from > simple spherical ions you've got problems. > > David Mobley > > > > On Fri, Dec 16, 2011 at 6:41 AM, Justin A. Lemkul wrote: > >> >> >> bipin singh wrote: >> >>> Hello, >>> >>> I am

[gmx-users] Regarding free energy calculation

are on in state B -- --- 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 pos

Re: [gmx-users] Unit of r in radial distribution function

Thanks. On Wed, Nov 30, 2011 at 20:06, Tsjerk Wassenaar wrote: > Hi Bipin, > > Gromacs uses nm. > > Cheers, > > Tsjerk > > On Wed, Nov 30, 2011 at 3:32 PM, bipin singh wrote: >> Hello, >> >> Please let me know what is the unit of r (nm or A) in

[gmx-users] Unit of r in radial distribution function

Hello, Please let me know what is the unit of r (nm or A) in the radial distribution function output(rdf.xvg) of the program g_rdf in gromacs. As the output shows no units. -- --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Regarding inter helical distance using g_bundle

Thanks for the suggestion. I will try that. On Tue, Nov 29, 2011 at 19:33, Gianluca Santoni wrote: > On 11/29/11 2:10 PM, bipin singh wrote: >> >> Hello, >> >> I want to calculate inter helical distance between two helices using >> g_bundle. As mentioned in the m

[gmx-users] Regarding inter helical distance using g_bundle

reference I am sending the link of figure with above Atom labels. http://researchweb.iiit.ac.in/~bipin.singh/helix.html Please have a look at the figure and provide your suggestions. --- Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.g

[gmx-users] Regarding cosine content

n the list a short while > ago regarding the interpretation of projections and cosine content. > Maybe they can help you form a picture of what is happening :) > > Hope it helps, > > Tsjerk > > > On Thu, Nov 17, 2011 at 12:22 PM, bipin singh wrote: >> Hello all, >&g

Re: [gmx-users] Regarding cosine content

n the list a short while > ago regarding the interpretation of projections and cosine content. > Maybe they can help you form a picture of what is happening :) > > Hope it helps, > > Tsjerk > > > On Thu, Nov 17, 2011 at 12:22 PM, bipin singh wrote: >> Hello all, >&g

[gmx-users] Regarding cosine content

respectively. What can be the reason for this huge difference in cosine content of the two proteins ? -- --- 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

Re: [gmx-users] High temperature Simulation

nt of side chains etc. On Mon, Oct 17, 2011 at 17:03, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> As far as I know we do energy minimization at room temperature only. > > Energy minimization is (theoretically) at 0 K, as there are no velocities > and it is

Re: [gmx-users] High temperature Simulation

>> (for a system of a protein in tip4p water) >> > > The set pressure should reflect whatever system you are trying to model. > > -Justin > >> Thank you >> With Regards >> Kavya >> >> On Mon, Oct 17, 2011 at 3:29 PM, bipin singh > <

Re: [gmx-users] High temperature Simulation

@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- --- 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/

Re: [gmx-users] CHARMM GUI to Gromacs

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

Re: [gmx-users] Implicit solvation

ch 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_Lists &g

[gmx-users] Regarding 1-d free energy profile from g_sham

st me whether it is possible through g_sham or not. -- --- *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 archi

[gmx-users] Regarding 1-d free energy profile from g_sham

st me whether it is possible through g_sham or not. -- --- *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/S

Re: [gmx-users] Identifying representative structures from a g_sham generated 2d energy plot

iling_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 > -- --- Regards, Bipin Sing

[gmx-users] Regarding clustering of MD data

gt; relevant or representative of the ensemble. I would suggest clustering > But you should only have a limited number of structures for a given point > (pc1,pc2), so why not just visualize the ensemble? > > Hope it helps, > > Tsjerk > > On Sep 10, 2011 8:02 AM, &quo

[gmx-users] Representative structure from MD trajectories

gt; relevant or representative of the ensemble. I would suggest clustering > But you should only have a limited number of structures for a given point > (pc1,pc2), so why not just visualize the ensemble? > > Hope it helps, > > Tsjerk > > On Sep 10, 2011 8:02 AM, &quo

Re: [gmx-users] Representative structure from MD trajectories

gt; relevant or representative of the ensemble. I would suggest clustering > But you should only have a limited number of structures for a given point > (pc1,pc2), so why not just visualize the ensemble? > > Hope it helps, > > Tsjerk > > On Sep 10, 2011 8:02 AM, &quo

[gmx-users] Representative structure from MD trajectories

anks 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 list. Use the www

Re: [gmx-users] Regarding xpm2ps

Sir, Thanks a lot for your help..Its working... On Wed, Aug 24, 2011 at 18:34, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Thanks for your kind help, >> I have tried as per your suggestion, the below command >> >> g_sham -f 2d_proj.xvg -xm

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

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

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