Amber Archive Jun 2018 by messages with attachments

343 messages: Starting Thu May 31 2018 - 22:30:02 PDT, Ending Sat Jun 30 2018 - 06:00:02 PDT
This period: Most recent messages
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[AMBER] high values of RMSD during the simulation of molecular dynamics between DNA and small molecule. Does anyone explain? Edjan Silva (Fri Jun 01 2018 - 07:26:20 PDT)
1. 06-01_10:43:30.png (118646 bytes)
Re: [AMBER] Accelerated MD re-weighting---- very high PMF values Chetna Tyagi (Sun Jun 03 2018 - 07:27:10 PDT)
1. 2D_Free_energy_surface.png (153669 bytes)
2. Dihed2.png (20183 bytes)
[AMBER] Amber DSSP : Secondary structure Garima Singh (Wed Jun 06 2018 - 04:17:18 PDT)
1. a.jpg (433780 bytes)
[AMBER] change x-axis to time for gnuplot using cpptraj Krantzman, Kristin D (Thu Jun 07 2018 - 12:19:09 PDT)
1. image001.png (18023 bytes)
2. image002.png (17454 bytes)
[AMBER] Fwd: Accelerated MD re-weighting---- very high PMF values Chetna Tyagi (Mon Jun 11 2018 - 05:33:42 PDT)
1. PC1-2.png (25009 bytes)
[AMBER] Change x-axis from frame # to time in gnu plot created with secstruct command using cpptraj Krantzman, Kristin D (Mon Jun 11 2018 - 12:07:31 PDT)
1. sec_Polyala_19_asn_g20.jpeg (46575 bytes)
[AMBER] Free Energy landscape (FEL) Facundo Gomes (Mon Jun 11 2018 - 19:58:46 PDT)
1. PCA1vsPCA2.png (70968 bytes)
2. DOI:_10.1073_pnas.0608432104.png (198533 bytes)
3. DOI:_10.1038_srep17421.png (285647 bytes)
[AMBER] why tleap adds TER in the middle of a DNA sequence Kat G (Wed Jun 20 2018 - 11:40:52 PDT)
1. 5mer.pdb (12970 bytes)
2. tleap.pdb (10875 bytes)
3. db.lib.dat (5287 bytes)
4. min.pdb (13185 bytes)
[AMBER] Problem in Membrane Simulation : water molecules are out of box somdev pahari (Thu Jun 21 2018 - 07:21:45 PDT)
1. snap.pdf (183052 bytes)
Re: [AMBER] Problem regarding running independent parallel simulations in AMBER14 using -rem<#> RITUPARNA ROY (Mon Jun 25 2018 - 08:43:52 PDT)
1. job.254990.err (2391 bytes)
[AMBER] Time averaged mean squared displacement Christopher Faulkner (Mon Jun 25 2018 - 08:50:34 PDT)
1. MSD.png (9243 bytes)
Re: [AMBER] rism1d query Rakesh Srivastava (Wed Jun 27 2018 - 03:24:28 PDT)
1. TP3_NaCl.inp (490 bytes)