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

-- *--- 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 list

[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

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 jalem...@vt.edu wrote: On 10/7/13 10:46 AM, bipin singh wrote: Hello All, I have calculated the distance between the binding pocket of protein

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

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 jalem...@vt.edu wrote: On 10/7/13 1:39 PM, bipin singh wrote: Thanks for the reply Dr. Justin. I have also thinking of the same possibility

[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

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

der Spoel sp...@xray.bmc.uu.sewrote: 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 of 0.3nm for RMSD calculation, I was expecting

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

31, 2013 at 9:45 AM, bipin singh bipinel...@gmail.com 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 should write the snapshots having RMSD greater than 0.3nm

[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 jalem...@vt.edu 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. tpbconv -h, particularly point 3. -Justin

[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

singh bipinel...@gmail.com 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_hbond to calculate H-bonds for a trajectory made from several

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

the 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 jalem...@vt.edu 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 trjconv, using the following

[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] 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 sp...@xray.bmc.uu.sewrote: 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 individual snapshots from MD

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

PM, Justin Lemkul jalem...@vt.edu 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 that this can be done with help of g_traj, but my concern is whether

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 jalem...@vt.edu 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-Ncons)/3N. Please let me

[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] Doubt about the Gromacs versions

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

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

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 know which one is the recent version of gromacs (with latest bugfixes) among the below. 4.5.7 and 4.6.1 And what

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

-X bond 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 bipinel...@gmail.com wrote: Thanks for your reply. Actually I am interested to see how much

[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

: Hi Bipin Singh, That indeed gives you the RMSD against the average. Do think about it a bit more: do you want the average of the whole structure, or should you account for a phase of relaxation? Cheers, Tsjerk On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul jalem...@vt.edu wrote

[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

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

://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/Search before

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

. * 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

[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 list

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

, bipin singh wrote: Hi All, I have a doubt regarding the calculation of number of contacts between two groups. Because, I am getting different number of contacts calculated through g_hbond -contact option and g_mindist -on option. I have used same cutoff for distance (0.6nm) in both the cases

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 er...@xray.bmc.uu.se 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 the reply

[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.

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 and Regards, Bipin Singh* -- gmx-users mailing listgmx

[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] 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

okt 2012 kl. 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 found any significant clue. At present, there is no way to do

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

Thanks for the information. On Thu, Nov 1, 2012 at 10:56 PM, Justin Lemkul jalem...@vt.edu 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 modified code in the user

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

/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/Search before posting! * Please don't post (un)subscribe

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

along 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 bipinel...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, November 1, 2012 1

[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 http

[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] 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

Re: [gmx-users] MD after equilibration phase

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/Search before posting

Re: [gmx-users] MD after equilibration phase

...@vt.edu 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 files). Ideally it should complain

Re: [gmx-users] MD after equilibration phase

, bipin singh wrote: When we mention gen_vel=no ;And provide pdb as input with no velocities As mentioned in the manual: The velocities are set to zero when there are no velocities in the input structure file Please elaborate what does this sentence mean. Each atom must have a velocity

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 mark.abra...@anu.edu.au wrote: On 7/04/2012 12:37 AM, Justin A. Lemkul wrote: bipin singh wrote: Thanks for your comments. One more question. Does Gromacs saves velocities

[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,* Bipin

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 jalem...@vt.edu wrote: bipin singh

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

, bipin singh wrote: Thanks for the reply. * *I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines? which depends more on the environment of the computer architecture and other variables of mdrun rather

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 jalem...@vt.edu wrote: bipin singh wrote: Thanks for the reply. / /I read the link. So, how one can predict something reliable using these results(based on 50ns in my

[gmx-users] Pressure coupling doubt

=no 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

) As 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

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

)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 Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

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 jalem...@vt.edu wrote: bipin singh wrote: Thanks again For the record, I didn't ask that you send me your files so I could troubleshoot for you

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

# --- Please provide your comments. On Tue, Mar 27, 2012 at 03:20, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Thanks for your reply. Yes, you are right that these topologies are self supporting and there is no need to to call any

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

provide suggestions. On Tue, Mar 27, 2012 at 17:59, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Thanks for your inputs. I have followed your suggestion and included the .itp for the octane molecule (containing atomtype definition for new atoms) in the topology file(.top

[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 list

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 sp...@xray.bmc.uu.se wrote: On 2012-03-26 13:55, bipin singh wrote: Hello all, I am using the GAFF topology provided for octan-1-ol at Gromacs liquid database (http

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

On Mon, Mar 26, 2012 at 18:46, Justin A. Lemkul jalem...@vt.edu 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 incorporate the information from

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

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 -- --- Regards, Bipin

[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

Re: [gmx-users] Regarding DispCorr

...@anu.edu.au wrote: 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 http://lists.gromacs.org/mailman/listinfo/gmx-users

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 mark.abra...@anu.edu.au 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 free energy calculation

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 jalem...@vt.edu wrote: bipin singh wrote: Hello, I am willing to study the free energy of binding of a cation (Ca++) to the protein and I am following the free

[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 post (un

[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] Unit of r in radial distribution function

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

[gmx-users] Regarding inter helical distance using g_bundle

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.gromacs.org

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 gianluca.sant...@ibs.fr 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 manual that g_bundle

[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] Regarding cosine content

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 bipinel...@gmail.com wrote: Hello all, I have done PCA from 50ns long trajectory

[gmx-users] Regarding cosine content

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 bipinel...@gmail.com wrote: Hello all, I have done PCA from 50ns long trajectory

Re: [gmx-users] Implicit solvation

://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 -- --- Regards, Bipin Singh -- gmx

Re: [gmx-users] CHARMM GUI to Gromacs

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 Singh -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] High temperature 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.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www

Re: [gmx-users] High temperature Simulation

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 bipinel...@gmail.com mailto:bipinel...@gmail.com wrote:    As far as I know we do energy minimization at room

Re: [gmx-users] High temperature Simulation

chains etc. On Mon, Oct 17, 2011 at 17:03, Justin A. Lemkul jalem...@vt.edu 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 not a true dynamical process. Only

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

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 archive

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

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/Search

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

. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- --- Regards, Bipin Singh IIIT-Hyderabad INDIA -- 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] Representative structure from MD trajectories

that is 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, bipin singh bipinel...@gmail.com wrote: Hello

[gmx-users] Regarding clustering of MD data

that is 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, bipin singh bipinel...@gmail.com wrote: Hello

[gmx-users] Representative structure from MD trajectories

, 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 send

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

that is 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, bipin singh bipinel...@gmail.com wrote: Hello

Re: [gmx-users] Regarding xpm2ps

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

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 jalem...@vt.edu wrote: bipin singh wrote: Hello, I am using the below .m2p file as input for xpm2ps

Re: [gmx-users] Regarding xpm2ps

: bipin singh wrote: Hello, I am using the below .m2p file as input for xpm2ps, but not able to get axis range label. What axis range do you obtain?  If your data do not actually span from -4 to 4, there's not much you can do.  I was assuming you had data that did fit this range.  You also

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 jalem...@vt.edu 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 -xmin -5 -xmax 5 -ls gibbs.xpm

[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

[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 interface

[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 interface

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 lina.lastn...@gmail.com wrote: On Sat, Aug 13, 2011 at 3:36 PM, bipin singh bipinel...@gmail.com wrote: Hello, Please let me know from

[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

[gmx-users] PCA and Free energy landscape

on this 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 PCA and Gibbs Free energy landscape

on this 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] 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] Concatenating two trajectories

the 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 jalem...@vt.edu wrote: bipin singh wrote: Hello, I want concatenate two trajectories which have same number of frames

Re: [gmx-users] Concatenating two trajectories

Thanks Sir, I understood... On Wed, Jul 20, 2011 at 16:46, Justin A. Lemkul jalem...@vt.edu 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 are the same, then the second trajectory

[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 requests

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

: Discussion list for GROMACS usersgmx-users@gromacs.org 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 chains A and B and the backbone rmsd between the two chains is 0.33A. My problem is that how

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