Re: [gmx-users] gmx trjconv -center not working?

that show this behavior. Rajat On Fri, 8 Feb 2019, 5:27 pm Justin Lemkul > > On 2/8/19 5:17 AM, Rajat Desikan wrote: > > Hi Mala, > > Please combine -center with "-pbc mol -ur compact" and check. > > Compact unit cell representation is only useful for dode

Re: [gmx-users] gmx trjconv -center not working?

Hi Mala, Please combine -center with "-pbc mol -ur compact" and check. Regards, Rajat -- Dr. Rajat Desikan Invictus Oncology, Delhi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

Re: [gmx-users] Problems during installation

: > On Mon, Jul 16, 2018 at 7:43 PM Rajat Desikan > wrote: > > > Hi Mark, > > > > Thank you for the quick answer. My group is experimenting with a > GPU-heavy > > processor-light configuration similar to the Amber machines available > from > > Exxact (

Re: [gmx-users] Problems during installation

Justin, Lovely advice. I'll definitely consider it :) Thank you. Regards, Rajat On Mon, Jul 16, 2018 at 11:15 PM Justin Lemkul wrote: > > > On 7/16/18 1:42 PM, Rajat Desikan wrote: > > Hi Mark, > > > > Thank you for the quick answer. My group is experimenting with

Re: [gmx-users] Problems during installation

on, Jul 16, 2018 at 6:47 PM Rajat Desikan > wrote: > > > Dear all, > > I'm trying to install openmm enabled version of gromacs 4.6.7 on a 6-core > > i7 machine with two GTX 1080 Ti GPUs. I am repeatedly facing a rather > > strange error while running make: > > > &

[gmx-users] Problems during installation

kefile:162: recipe for target 'all' failed make: *** [all] Error 2 I have installed cuda 9.1, openmm, fftw, open-mpi and all other necessary software, so I'm at a loss. Please help me out. Google did not have much leads. Thank you. Regards, Rajat -- Dr. Rajat Desikan (Post Doctoral Fellow) Prof.

Re: [gmx-users] Unable to install 5.1.14

her possibility is to downgrade boost to older, but you can bump into > other mish-mash issues. I do not recommend that. > > > > On Sunday, August 27, 2017, 11:36:21 PM GMT+3, Rajat Desikan < > rajatdesi...@gmail.com> wrote: > > Dear All, > I had removed gromacs 5

[gmx-users] SASA with rhombic dodecahedron

. Is there any way to go about this? Repeating the simulation is unfortunately not an option. Thanks. Regards, -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search

Re: [gmx-users] SASA with rhombic dodecahedron

, 2014 at 9:49 AM, rajat desikan rajatdesi...@gmail.com wrote: Dear All, SASA calculations of a solvated protein in a rhombic dodecahedron gives the following warning: WARNING: non-rectangular boxes may give erroneous results or crashes. Analysis based on vacuum simulations

Re: [gmx-users] SASA with rhombic dodecahedron

. Regards, On Mon, Nov 10, 2014 at 6:36 PM, rajat desikan rajatdesi...@gmail.com wrote: Thank you, Tsjerk. I will take a look. Are there any compatibility issues with a 4.6.4 trajectory and GMX 5 analysis tools? On Mon, Nov 10, 2014 at 4:04 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi

Re: [gmx-users] Making index file

/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org javascript:;. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] Making index file

On Wed, Nov 5, 2014 at 2:27 PM, rajat desikan rajatdesi...@gmail.com javascript:; wrote: Hi, As an example, assuming that I have four chains (A,B,C,D) and want to select residue 14 in chains A,B and D 1 r 14 chain A|1 r 14 chain B| 1 r 14 chain D

Re: [gmx-users] Naughty Vacuum Bubble in our Vesicle!

://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org javascript:;. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing

Re: [gmx-users] Naughty Vacuum Bubble in our Vesicle

. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Regarding msd

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Re: [gmx-users] Regarding msd

trajectory). Since Pratibha wants to test her own code, the way she treats pbc is something to keep in mind. On Wed, Oct 8, 2014 at 4:59 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/8/14 3:21 AM, rajat desikan wrote: Hi, You need to use -pbc nojump to calculate the msd. Using -pbc whole

Re: [gmx-users] adding ions in the genion for multimeric proteins

://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Rajat Desikan

Re: [gmx-users] How to combine Slipid FF with amber FF?

/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive

Re: [gmx-users] How to combine Slipid FF with amber FF?

Hi, I assumed that you had gone through the forcefield.ff files on Slipids webpage. You need to include the following section at the end in your ffnonbonded.itp (some of the spaces may be missing below). I suggest modifying a local copy of your desired Amber ff. ; SLIPIDS STARTS HERE HAL11

Re: [gmx-users] gromacs

/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Rajat Desikan (Ph.D

Re: [gmx-users] Plotting hydrogen bonds and salt bridges.

...@gromacs.org. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

Re: [gmx-users] g_sas

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Re: [gmx-users] g_sas

Hi Eric, Sorry, I misread your mail. You cannot compute the vacuum accessible surface area for a liquid because the molecules are in constant motion. Regards, On Sat, Aug 16, 2014 at 9:15 PM, rajat desikan rajatdesi...@gmail.com wrote: Hi Eric, 1) Yes. Use a probe radius of 0 nm. 2

Re: [gmx-users] g_sas

or not that output is meaningful to you is up to you; I have never dealt in vacuum-accessible SA. -Justin Thanks again Rajat, Best, Eric Message: 7 Date: Sat, 16 Aug 2014 21:17:36 +0530 From: rajat desikan rajatdesi...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org

Re: [gmx-users] Simulation at high temperature

/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] pH simulation

...@gromacs.org. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

Re: [gmx-users] Problems with trajectories

. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

Re: [gmx-users] Citing gromacs tools

Thank you for the clarification, Prof. David. On Tuesday, May 13, 2014, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2014-05-13 07:52, rajat desikan wrote: Hi All, In many papers, the authors cite the main gromacs paper and simply declare in the methods section that they used

[gmx-users] Citing gromacs tools

--- Thank You --- -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

Re: [gmx-users] vdw radii in g_sas

is different from that for P alone. Cheers, Tsjerk On May 9, 2014 10:53 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/9/14, 3:35 PM, rajat desikan wrote: Thanks Justin. I am curious about the value for a phosphorus atom (protein in phospholipid bilayer; g_sas issues a warning). Do you

[gmx-users] vdw radii in g_sas

ffnonbonded values? I would love to hear your thoughts/suggestions. Thanks, -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] Regarding the comparison of two result

to gmx-users-requ...@gromacs.org. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX

Re: [gmx-users] Regarding the comparison of two result

I forgot to mention that the earlier simulations were with version 4.5.4 On Fri, May 2, 2014 at 6:13 PM, rajat desikan rajatdesi...@gmail.comwrote: Hi, I would suggest caution. I had a DPPC bilayer interacting with organic molecules (beta naphthol) which are supposed to alter the phase

[gmx-users] g_potential help

. g_potential returns the result for epsilon_r = 1. How can I incorporate this into the result? 2) Default ng =1? Is the number of groups referring to the number of charge groups defined in the topology? Thank you for your time. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13

Re: [gmx-users] g_potential help

g_potential literally? Thanks, On Monday, April 21, 2014, Justin Lemkul jalem...@vt.edu wrote: On 4/21/14, 9:58 AM, rajat desikan wrote: Hi All, I have a membrane-protein-solvent system, and I want the potential across the membrane in the direction of the membrane normal. I have 2

Re: [gmx-users] strange do_dssp error

Update for anyone interested: Installing dssp 2.2.1 solved the above error! I am not sure why... On Sun, Feb 9, 2014 at 11:39 AM, rajat desikan rajatdesi...@gmail.comwrote: Hi All, I get this error while running do_dssp. The program reads the whole trajectory but fails to write a scount file

Re: [gmx-users] g_helixorient help

(by dividing the vector by their norm) and calulate their # dot-product in excel. # The dot product of two normalized vectors is the cosine of their # cross-angle. Disclaimer: Copied from an old gromacs discussion. On Thu, Jan 30, 2014 at 2:06 PM, rajat desikan rajatdesi...@gmail.com wrote

Re: [gmx-users] g_helixorient help

Hi All, Any suggestions? Thanks. On Mon, Jan 27, 2014 at 5:01 PM, rajat desikan rajatdesi...@gmail.comwrote: Hi All, I am trying to calculate the angle between the axes of two alpha helices (say A and B) in my simulation. I have separate index files for the residues pertaining to each

[gmx-users] g_helixorient help

-nxy shows 27 data sets. What do these correspond to? (Helix A has 34 residues). Similarly for bending_A.xvg How do I go about this? Is this the right way to calculate the relative helix axis angle? Thanks, -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept

Re: [gmx-users] LR electrostatics in single point energy calculations

is the reciprocal space term in a Ewald summation calculation, right? I want the total potential energy of the protein. How would I go about that? Thanks. On Wed, Jan 15, 2014 at 7:39 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/15/14, 7:14 AM, rajat desikan wrote: Hi All, I was wondering about

Re: [gmx-users] non-native contatcs

https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list

Re: [gmx-users] Calculating atom charges for ester

-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Rajat Desikan (Ph.D Scholar) Prof. K

[gmx-users] Strange trjconv error

}... Any idea about how to proceed. I am quite stumped. Thanks. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] Strange trjconv error

next time... On Tue, Dec 10, 2013 at 8:28 PM, Justin Lemkul jalem...@vt.edu wrote: On Tue, Dec 10, 2013 at 8:55 AM, rajat desikan rajatdesi...@gmail.com wrote: Hi All, I have a NPT NAMD trajectory of a membrane-protein that I want to analyze in gromacs 4.6.3. (g_density). I used catdcd

Re: [gmx-users] heating

before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy

Re: [gmx-users] Coulombic potential modifiers in Gromacs 4.6.4.

...@gmail.comwrote: On Nov 21, 2013 9:20 AM, rajat desikan rajatdesi...@gmail.com wrote: Hi All, I was wondering about the coulomb-modifier = Potential-shift-Verlet option in conjunction with the Verlet cut-off scheme and PME. I can understand that vdw-modifier = Potential-shift