[gmx-users] Regarding parameters for Bromine ion in Charmm36 FF

-) anions in charmm36 FF...? Any suggestions are highly appreciated. Thank you. --- With Best Regards, *Dilip.H.N* Ph.D Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mailtrack.io?u

[gmx-users] Cannot flush logfile - maybe you are out of disk space?

e 4156600083132.0 Now i have made the disk-free and still, the simulation is still struck. So now may i know how can i proceed..?? Any suggestions are highly appreciated. Thank you. --- With Best Regards, *Dilip.H.N* Ph.D Student. [image: Mailtrack] <https://mailtrack.io?utm_source

Re: [gmx-users] Amide hydrogen naming in charmm 36 forcefield

l fix that for the future." and hence i changed the 'H' into 'HN'. In spite in both the cases (naming the amide hydrogens as 'H' or 'HN'), i am getting the errors. The amide nitrogens are not defined in the .hdb files in charmm36 FF too. Any suggestions...? Thank you. --- With Best Regards,

[gmx-users] Amide hydrogen naming in charmm 36 forcefield

ted. Thank you. --- With Best Regards, Dilip.H.N Ph.D. Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signatureviralit

[gmx-users] Relative constraint deviation after LINCS:

resolve this issue..? Thank you. --- With Best Regards, Dilip.H.N Ph.D. Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature

[gmx-users] Broken bonds between peptide and capped terminals when solvated

, Dilip.H.N Ph.D. Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> 27/05/19, 10:33:05 -- Gromacs Users

[gmx-users] Unusual bond between residues which are capped

and 9 (none) is the N-methyl group which are capped to the protein C and N terminals. How can i solve this issue..?? Any suggestions? Thank you. --- With Best Regards, Dilip.H.N Ph.D. Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campa

[gmx-users] Different models of TMAO

models required to run the simulations... How can i include the epsilon and LJ parameters in it...? Any suggestions are appreciated. Thank you. --- With Best Regards, Dilip.H.N Ph.D. Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirali

[gmx-users] Different models of TMAO

models required to run the simulations... Any suggestions are appreciated. Thank you. --- With Best Regards, Dilip.H.N Ph.D. Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mai

[gmx-users] Residue id of capped peptide getting changed when adding molecules

are shown as "Warning) Unusual bond between residues: 1(none) and 2 (protein) Warning) Unusual bond between residues: 2 (protein) and 3 (none)" when viewed in VMD. causing a problem... Any suggestions are highly appreciated. Thank you. --- With Best Regards, Dilip.H.N Ph.D. Student. [imag

[gmx-users] Regarding rigidity of water models

to calculate the power spectrum of the water (which can give more insights...). How can i do it in GROMACS..?? Any suggestions are highly appreciated. Thank you. --- With Best Regards, Dilip.H.N PhD Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campa

Re: [gmx-users] Distance between the atoms greater than Box length

. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> 06/05/18, 10:34:06 AM --- With Best Regards, Dilip.H.N PhD Student. O

Re: [gmx-users] Distance between the atoms greater than Box length

mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> 06/04/18, 5:26:50 PM --- With Best Regards, Dilip.H.N PhD Student. On Mon, Jun 4, 2018 at 5:15 PM, Dilip.H.N wrote: > Hello all, > I have extracted the trajectory of my system containing all the water > mol

[gmx-users] Distance between the atoms greater than Box length

7SOLHW2 18 -0.064 2.126 0.245 --- With Best Regards, Dilip.H.N PhD Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature

Re: [gmx-users] Regarding calculation of SDF

, 9:26:54 AM --- With Best Regards, Dilip.H.N PhD Student. On Mon, May 28, 2018 at 7:47 AM, Dilip.H.N wrote: > Hi, > I want to calculate the Spatial Distribution Function of say N-terminal > nitrogen atom and all the oxygen atoms of the water molecules. > So, i have created the in

[gmx-users] Regarding calculation of SDF

SDF/it is wired when i give an isovalues and change its values... How can i solve this..?? Any suggestions are highly appreciated. Thank you. --- With Best Regards, Dilip.H.N PhD Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirali

[gmx-users] Regarding getting good performance for mdrun

Thank you. --- With Best Regards, Dilip.H.N PhD Student. -- 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 v

Re: [gmx-users] Regarding getting the coordinates within certain region of amino-acid

il_medium=signature_campaign=signaturevirality3;> --- With Best Regards, Dilip.H.N PhD Student. On Thu, Apr 12, 2018 at 1:48 PM, Joe Jordan <e.jjorda...@gmail.com> wrote: > Since gmx trjconv does not work with dynamic selections, you can either > feed the index file to trjconv

Re: [gmx-users] Regarding getting the coordinates within certain region of amino-acid

; Sent with Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality;> --- With Best Regards, Dilip.H.N PhD Student. On Thu, Apr 12, 2018 at 1:12 PM, Joe Jordan <e.jjorda...@gmail.com> wrote: > You need -on for gmx select to write out the index

Re: [gmx-users] Regarding getting the coordinates within certain region of amino-acid

hin 3.5 nm of the nitrogen atom of glycine molecule for each time frame. Any suggestions are appreciated. Thank you. ‌ <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality;> --- With Best Regards, Dilip.H.N PhD St

[gmx-users] Regarding getting the coordinates within certain region of amino-acid

Hello all, I want to get the water molecules which are at a certain distance (say all the water molecules which are within 0.35nm of the Nitrogen atom of glycine molecule). How can i get this all the coordinates.? Any specific commands..?? Thank you. --- With Best Regards, Dilip.H.N PhD