Re: [gmx-users] Position restrain of of different chain in fibril structure

after the energy minimization. When i run the nvt.mdp then the fibril structure broken. All chain aligned one by one. Best regards Md Imrul Reza Shishir On Tue, Jun 7, 2016 at 10:19 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/6/16 9:13 PM, Md. Imrul Reza Shishir wrote

[gmx-users] Position restrain of of different chain in fibril structure

the position of my structure. In the dropbox link i attached nvt.mdp, npt.mdp, md.mdp and also Input and output structure image in vmd. https://www.dropbox.com/sh/skkskzp1pruf227/AADI2a7TG6pzadFzIEE8094na?dl=0 Thank you very much. -- *Md Imrul Reza Shishir* Master Student *Inha University* -- Gromacs

Re: [gmx-users] Position restrain of structure

://www.dropbox.com/sh/skkskzp1pruf227/AADI2a7TG6pzadFzIEE8094na?dl=0 Thank you very much. Best regards Md Imrul Reza Shishir On Fri, Jun 3, 2016 at 6:45 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/1/16 11:22 PM, Md. Imrul Reza Shishir wrote: > >> Dear all &g

[gmx-users] Position restrain of structure

= no; for position restrain this is the right way. Or I have to do something else. Actually my main target to retrain the fibril structure and 36 chain are formed 7 sheet not a single chain like structure. ​Thank you very much.​ -- *Md Imrul Reza Shishir* Master Student *Inha University* -- Gromacs

[gmx-users] pdb2gmx illegal instruction (core dumped)

uot;. And in my directory only topology file create. No gromacs output file Created "1AKI_processed.gro". Any help greatly appreciated. ​Bst Regards​ -- MD IMRUL REZA SHISHIR ​Inha University​ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mai

Re: [gmx-users] pdb2gmx illegal instruction (core dumped)

Thank you David van der Spoel. I compile gromacs in my own laptop and I run on the same machine. Your guideline working properly. I reinstall gromacs and now all okk.. regards and thank you. Md Imrul Reza Shishir On Jan 28, 2016 4:47 PM, "David van der Spoel" <sp...@xray.bmc

[gmx-users] Adding Residue in .rtp file.

to add residue in gromacs in details. -- *Md Imrul Reza Shishir* -- 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

Re: [gmx-users] Installation Problem... No command 'gmx' found

>> Regards, >> >> >> Husen >> >> On 21 Apr 2016, at 12.31, terrence...@gmail.com wrote: >>> >>> Hi, >>> >>> Try gmx_mpi. >>> >>> Regards >>> Terry >>> >>> >>> On 21 Apr 2016, at 12:1

[gmx-users] Residue not found in residue topology database

sidue GLCB is show there as LCB. And how I solve this. -- *Md Imrul Reza Shishir* Master Student *Inha University* *CRC for NanoCellulose Future Composites* 36 Getbeol-ro, Yeonsu-gu Incheon 21999 South Korea -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.o

[gmx-users] Starting residue "XXX"in chain not identified as Protein/RNA/DNA.

ngles, dihedrals and pairs... Before cleaning: 54 pairs Before cleaning: 61 dihedrals Making cmap torsions... There are 44 dihedrals,9 impropers, 39 angles 48 pairs, 29 bonds and 0 virtual sites Total mass 324.286 a.m.u. Total charge -0.000 e " -- *Md Imrul Reza Shish

[gmx-users] Installation Problem... No command 'gmx' found

In the installation procedure i dont find any error. All 26 test completed without error. But when i try to run "gmx or gmx help" There is error no command gmx found. I need your guidance. ​Best Regards -- *Md Imrul Reza Shishir* -- Gromacs Users mailing list * Please search the archiv

[gmx-users] How to define two different constraint algorithms for different group

Dear all I want to define LINCS algorithms for my system and SETTLE algorithms for my solvent. How we should define that. Is there any tutorial or guideline for this. ​Thank you very much.​ -- *Md Imrul Reza Shishir* -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] relative reorientation calculation

). -- *Md Imrul Reza Shishir* Master Student *Inha University* *CRC for NanoCellulose Future Composites* 36 Getbeol-ro, Yeonsu-gu Incheon 21999 South Korea -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

[gmx-users] Analysis pull code simulation data to obtain Strain Stress curve

confused how I can obtain strain-stress curve from this simulation data. I want some guidance about this purpose. Thank you very much -- *Md Imrul Reza Shishir* Master Student *Inha University* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Analysis pull code simulation data to obtain Strain Stress curve

for the response. And wish some guidance. Best Regards Md Imrul Reza Shishir On Fri, Mar 24, 2017 at 5:35 PM, Alex <nedoma...@gmail.com> wrote: > Hi there, > > Everyone is confused about how to get stress-strain curves from Justin's > tutorial. Because it has nothing to do with nanome

[gmx-users] How to measure distance between two COM (centre of mass) of two group of atom

. ​ "gmx distance -s *.tpr -f *.gro -n index.ndx -oall *.xvg​" ​Is this process is correct? What else should be the right procedure. I am little bit confused with the output xvg file result. From where how can I measure the distance.​ -- *Md Imrul Reza Shishir* Master Student *Inha

[gmx-users] Density calculation

of time period or distribution. ​Thanks in advance.​ ​ ​ -- *Md Imrul Reza Shishir* Master Student *Inha University* -- 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/Su

[gmx-users] Unit cell parameter and molecule volume calculation

temperature which I simulate. how will I get the final unit cell parameter and density of the system? -- *Md Imrul Reza Shishir* Master Student *Inha University* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] Check for bad contacts and/or reduce the timestep

. ​ -- *Md Imrul Reza Shishir* Master 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 visit https

[gmx-users] dihedral angle calculation of glycosidic bond

4 63 0.408 7.377 9.202 -0.1907 -0.1807 -0.1760 Thank you very much best Regards Md iMrul Reza Shishir -- 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/Su

[gmx-users] how to select index group in gmx hbond or any other command

group several time. I want to make script file with all the command. Is it possible to add group selection in the script file. Otherwise i have to select the group every time in the terminal which is hilarious work for like 100 command. -- *Md Imrul Reza Shishir* Master Student ​​ -- Gromacs Users

[gmx-users] how to pull both direction with constant force

; simple distance increase pull_coord1_groups = 1 2 pull_coord1_dim = N N Y pull_coord1_k = -7000 ; kJ mol^-1 nm^-1 pull_coord1_start = yes ; define initial COM distance > 0 -- *Md Imrul Reza Shishir* Master Student *Inha University* *

[gmx-users] hydrogen bond analysis

uot;Hydrogen bonds" @ s1 legend "Pairs within 0.35 nm" 0 7 11 0.001 8 10 0.002 7 11 0.003 6 12 0.004 7 11 ​"""""" Thank you very much