Re: [gmx-users] Simulation at high temperature

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 Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of

Re: [gmx-users] g_sas

Best, > Eric > -- > 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 http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit >

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 wrote: > Hi Eric, > 1) Yes. Use a probe radius of 0 nm. > 2) No. There is n

Re: [gmx-users] g_sas

> This should not be necessary; you can provide the trajectory and g_sas > should do this for you. Whether 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, >>

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

n)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 Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, B

Re: [gmx-users] gromacs

http://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-u

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

st? 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 Ayappa's Lab (no 13), D

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] adding ions in the genion for multimeric proteins

cribe 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 Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Banga

Re: [gmx-users] Regarding msd

rt/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 . &

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 wrote: > > > On 10/8/14 3:21 AM, rajat desikan wrote: > >> Hi, >> You need to use -pbc nojump to calculate the msd. Usin

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

> * Please search the archive at http://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/mail

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

gt; > * 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 Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute

Re: [gmx-users] Making index file

ww.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 Ayappa's Lab (no 1

Re: [gmx-users] Making index file

A using the following command, I get 10 atoms, but I should > get > > > only 1 atom. > > > > > > r 14 & a CA & chain A. > > > > > > It means that the tool is taking CA of residue 14 from all 10 chains.. > > > > > > Still the pro

[gmx-users] SASA with rhombic dodecahedron

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 searc

Re: [gmx-users] SASA with rhombic dodecahedron

; On Mon, Nov 10, 2014 at 9:49 AM, rajat desikan > 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 cr

Re: [gmx-users] SASA with rhombic dodecahedron

hanks. Regards, On Mon, Nov 10, 2014 at 6:36 PM, rajat desikan 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 > wrote: > >> Hi Raj

[gmx-users] Problems during installation

les/mdrun.dir/all] Error 2 Makefile: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.

Re: [gmx-users] Problems during installation

> > On Mon, 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 ma

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

Re: [gmx-users] Problems during installation

áll wrote: > 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 > >

[gmx-users] Unable to install 5.1.14

DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs514 -DGMX_USE_RDTSCP=off I've tried other permutations of the above command (without -DGMX_USE_RDTSCP=off for instance) and nothing seems to work. Thank you for your time. Regards, Rajat -- Dr. Rajat Desikan

Re: [gmx-users] Unable to install 5.1.14

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 5.1.14. from my system (Ubuntu 16

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&#x

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

tach test files 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 use

Re: [gmx-users] nstlist and performances

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 > > > -- > gromacs.org_gmx-users mailing list > gromacs.org_gmx-users@maillist.sys.kth

Re: [gmx-users] nstlist and performances

)? Thanks, On Tue, Nov 19, 2013 at 4:52 PM, Mark Abraham wrote: > On Tue, Nov 19, 2013 at 6:12 AM, rajat desikan >wrote: > > > Hi, > > I would be very careful about increasing nstlist for big systems. This > can > > lead to nonphysical phenomena, especially

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

. What does the coulomb-modifier do? We are accounting for the long range coulombic interactions using reciprocal space sums in PME, right? What exactly is the shift here? Thanks -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institu

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

03 PM, Mark Abraham wrote: > On Nov 21, 2013 9:20 AM, "rajat desikan" wrote: > > > > Hi All, > > > > I was wondering about the coulomb-modifier = Potential-shift-Verlet > option > > in conjunction with the Verlet cut-off scheme and PME. > &g

Re: [gmx-users] heating

/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.

Re: [gmx-users] heating

t; > >> Department of Pharmaceutical Sciences > >> School of Pharmacy > >> Health Sciences Facility II, Room 601 > >> University of Maryland, Baltimore > >> 20 Penn St. > >> Baltimore, MD 21201 > >> > >> jalem...@outerbanks.umaryland.

[gmx-users] Trouble running 4.6.4. on cpu+gpu but not on gpu alone

troubleshooting, please check the GROMACS” -- 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_List

[gmx-users] Strange trjconv error

tomnumber= -1}... 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 th

Re: [gmx-users] Strange trjconv error

next time... On Tue, Dec 10, 2013 at 8:28 PM, Justin Lemkul wrote: > On Tue, Dec 10, 2013 at 8:55 AM, rajat desikan >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] Calculating atom charges for ester

gt; http://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 m

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

was wondering if there is a way to do it in Gromacs? 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://www.gromacs.org/Su

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

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 wrote: > > > On 1/15/14, 7:14 AM, rajat desikan wrote: > >> Hi All, >>

Re: [gmx-users] non-native contatcs

e search the archive at http://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/

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

11:57 AM, rajat desikan wrote: > >> Hi Justin, >> >> I meant the pairwise interaction energies and not the total potential >> energy (I >> plan to define a 'interaction energy' by summing up all the individual >> terms). I >> followed your

[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), Dep

Re: [gmx-users] g_helixorient help

Hi All, Any suggestions? Thanks. On Mon, Jan 27, 2014 at 5:01 PM, rajat desikan wrote: > 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

Re: [gmx-users] Molecular volume from trajectory

macs.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...@

Re: [gmx-users] g_helixorient help

inate of 3 points belonging to the second helix. > > # When this point is reached, you can define the vectors describing the > # helices (by substracting coordinate of atom 3 and 1 and atom 6 and 4), > # normalize them (by dividing the vector by their norm) and calulate their >

[gmx-users] strange do_dssp error

1000 r-xp 00:00 0 [vsyscall] Aborted (core dumped) -- 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/Suppo

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 wrote: > Hi All, > I get this error while running do_dssp. The program reads the whole > trajectory but fails to write a scount file. gmxche

[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 (

Re: [gmx-users] g_potential help

g_potential literally? Thanks, On Monday, April 21, 2014, Justin Lemkul 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

Re: [gmx-users] g_potential help

Thank you! On Tuesday, April 22, 2014, Justin Lemkul wrote: > > > On 4/21/14, 5:11 PM, rajat desikan wrote: > >> Hi Justin, >> >> So different parts of my system in Z-direction should be scaled >> differently, right? On a coarse level, aqueous part with

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

rs mailing list > > * Please search the archive at http://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/

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 wrote: > Hi, > I would suggest caution. I had a DPPC bilayer interacting with organic > molecules (beta naphthol) which are supposed to alter the phase behaviour. >

[gmx-users] vdw radii in g_sas

rom 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

Re: [gmx-users] vdw radii in g_sas

Thanks Justin. I am curious about the value for a phosphorus atom (protein in phospholipid bilayer; g_sas issues a warning). Do you know any reference for experimental values? On Friday, May 9, 2014, Justin Lemkul wrote: > > > On 5/9/14, 12:23 PM, rajat desikan wrote: > >>

Re: [gmx-users] vdw radii in g_sas

ntonio > > > On Fri, 9 May 2014, Tsjerk Wassenaar wrote: > > Do mind that the radius for P in PO4 is different from that for P alone. >> >> Cheers, >> >> Tsjerk >> On May 9, 2014 10:53 PM, "Justin Lemkul" wrote: >> >> >>&g

Re: [gmx-users] vdw radii in g_sas

Hi All, I am extremely sorry for the blooper in the above mail. I meant to write g_mdmat, but it came out as g_sas! Please give me any heuristic suggestions for choosing the truncation distance, if any. Thanks, On Sat, May 10, 2014 at 11:47 PM, rajat desikan wrote: > Thank you Justin, Tsj

[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

[gmx-users] g_mdmat truncation distance for contacts

suggestions about the truncation distance value? Thank you all for your time. 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 the archi

Re: [gmx-users] Citing gromacs tools

Thank you for the clarification, Prof. David. On Tuesday, May 13, 2014, David van der Spoel 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 u

Re: [gmx-users] Problems with trajectories

port/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 Ayappa's Lab (no 13), Dept. of Chemical Engin

Re: [gmx-users] pH simulation

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 * Please search the