Amber Archive Jul 2018 by thread
- [AMBER] Extraction of atomic charges. Vishal Kumar (Sun Jul 01 2018 - 05:32:44 PDT)
- [AMBER] Query about Salt-Concentration (soltcon) for Constant pH MD Bharat Manna (Sun Jul 01 2018 - 22:51:09 PDT)
- Re: [AMBER] eCheminfo Milano July 16-29, Training and Innovation Course in Drug Design 2018, bursary and early-bird deadline ending soon Thomas Exner (Mon Jul 02 2018 - 03:05:47 PDT)
- Re: [AMBER] Geforce GTX 1080Ti testing on Amber18/CUDA 9.2 Ross Walker (Mon Jul 02 2018 - 04:57:26 PDT)
- Re: [AMBER] Cuda Ross Walker (Mon Jul 02 2018 - 05:02:14 PDT)
- Re: [AMBER] Individual bridging water lifetimes by closest? Daniel Roe (Mon Jul 02 2018 - 06:25:19 PDT)
- [AMBER] Tutorial B1 problems Jennifer L. Muzyka (Mon Jul 02 2018 - 08:46:58 PDT)
- [AMBER] How to specify the protein position in box while using tleap Jinfeng Chen (Mon Jul 02 2018 - 18:15:25 PDT)
- [AMBER] How should I perform a long-time Simulated Annealing MD? xmgign.126.com (Tue Jul 03 2018 - 01:32:16 PDT)
- [AMBER] Tleap Impose Doesn't work for defining some angle/diedral Alechania Misturini (Tue Jul 03 2018 - 04:57:37 PDT)
- [AMBER] global scaling of vdW Korey M Reid (Tue Jul 03 2018 - 11:10:02 PDT)
- [AMBER] AMBER: QM/MM calculations using GPU Witkin, Katharine R (Tue Jul 03 2018 - 12:52:07 PDT)
- [AMBER] premed.cuda.MPI Shirin Jamshidi (Tue Jul 03 2018 - 16:40:40 PDT)
- [AMBER] pmemd.cuda.MPI Shirin Jamshidi (Tue Jul 03 2018 - 16:41:54 PDT)
- [AMBER] packmol error Gustaf Olsson (Wed Jul 04 2018 - 00:29:32 PDT)
- [AMBER] TI calculations emanuele (Wed Jul 04 2018 - 03:15:35 PDT)
- [AMBER] Ph.D. candidate position in biomolecular modeling or bioinformatics Jan Brezovsky (Wed Jul 04 2018 - 03:26:44 PDT)
- [AMBER] Regarding installation problem in CUDA 9.2 Debasish Mandal (Wed Jul 04 2018 - 03:37:39 PDT)
- [AMBER] How to reference the integration algorithm? Elisa Pieri (Wed Jul 04 2018 - 10:31:42 PDT)
- Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM PRITI ROY (Wed Jul 04 2018 - 12:52:43 PDT)
- [AMBER] Interpretation the result of pairwise per-residue MM/PB(GB)SA decomposition. walkingintheair (Wed Jul 04 2018 - 20:18:04 PDT)
- [AMBER] Error while perform ALA Scanning Mutageneis Mitul Srivastava (Thu Jul 05 2018 - 00:42:41 PDT)
- [AMBER] RST file setting in SMD Meng Wu (Thu Jul 05 2018 - 05:56:06 PDT)
- [AMBER] setting ionic strength in leap Kris Feher (Thu Jul 05 2018 - 13:45:26 PDT)
- [AMBER] Need help regarding Constant pH MD in pmemd.cuda Bharat Manna (Thu Jul 05 2018 - 23:37:08 PDT)
- [AMBER] huge difference in GB and PB energies calculated with MMPBSA.py Charles Mariasoosai (Fri Jul 06 2018 - 00:55:49 PDT)
- [AMBER] Need help regarding CpHMD with T-REMD Saikat Dutta chowdhury (Fri Jul 06 2018 - 03:52:10 PDT)
- [AMBER] Fit the trajectory to the original inpcrd file Meng Wu (Fri Jul 06 2018 - 05:40:31 PDT)
- [AMBER] Calcutaion of the observed acceptance ratio from simulation RITUPARNA ROY (Fri Jul 06 2018 - 06:07:46 PDT)
- [AMBER] Si bonded parameters GAFF compatible Alechania Misturini (Fri Jul 06 2018 - 11:17:23 PDT)
- [AMBER] Some Parameters In MM_PB/GBSA 龚乾坤 (Sat Jul 07 2018 - 04:10:07 PDT)
- [AMBER] Regarding simulation of Organometallic compounds dhaval patel (Sat Jul 07 2018 - 04:11:52 PDT)
- [AMBER] Energy file generation problem of pmemd.cuda Meng Wu (Sat Jul 07 2018 - 06:02:17 PDT)
- [AMBER] distance restraints and accelerated MD giulia palermo (Sun Jul 08 2018 - 17:08:00 PDT)
- [AMBER] Puckering parameters for pyranose ring Rajarshi Roy (Sun Jul 08 2018 - 22:40:34 PDT)
- [AMBER] The Calculate Formula of Ionic strength in MM_PBSA/GBSA 龚乾坤 (Mon Jul 09 2018 - 01:40:56 PDT)
- [AMBER] Question about equilibration of membrane protein MD 鲍劲霄 (Mon Jul 09 2018 - 02:14:56 PDT)
- [AMBER] How to provide the CPIN input file argument for CpHMD in pmemd.cuda? Bharat Manna (Mon Jul 09 2018 - 03:31:39 PDT)
- [AMBER] Help on Elisa Pieri (Mon Jul 09 2018 - 06:12:07 PDT)
- [AMBER] implicit solvent remd simulation Chhaya Singh (Mon Jul 09 2018 - 09:37:55 PDT)
- [AMBER] issues with accelerated MD in chloroform Chetna Tyagi (Mon Jul 09 2018 - 11:37:11 PDT)
- [AMBER] MM_PBSA/GBSA 龚乾坤 (Tue Jul 10 2018 - 04:51:15 PDT)
- [AMBER] Lipid NMR order parameters Christopher Faulkner (Tue Jul 10 2018 - 05:53:30 PDT)
- [AMBER] Xleap does not (?) loadoff lib files Sebastian Muraru (Tue Jul 10 2018 - 06:46:33 PDT)
- [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces Kandes, Martin (Tue Jul 10 2018 - 16:46:35 PDT)
- [AMBER] Ionic strength in MM_PBSA 龚乾坤 (Tue Jul 10 2018 - 19:39:35 PDT)
- [AMBER] PCA multiple trajectories for mutants and wild type Stejskal, Lenka (Wed Jul 11 2018 - 04:48:26 PDT)
- [AMBER] Regarding Force constants from Mopac Devashish_Das (Wed Jul 11 2018 - 09:30:22 PDT)
- [AMBER] H-REMD ligand binding Milo Westler (Wed Jul 11 2018 - 11:16:45 PDT)
- [AMBER] Cannot run pdb4amber Alen Ahmetovic (Wed Jul 11 2018 - 21:27:24 PDT)
- [AMBER] Replica Exchange with Solute Tempering implementation in AMBER14/16/18 on GPUs Alan Hicks (Thu Jul 12 2018 - 10:38:15 PDT)
- [AMBER] Error in MCPB.py step 2 dhaval patel (Thu Jul 12 2018 - 12:36:06 PDT)
- [AMBER] Amber16 to Amber18 upgrade? Hirdesh Kumar (Thu Jul 12 2018 - 13:46:13 PDT)
- [AMBER] peptide bond restraints lucrecia bogado (Thu Jul 12 2018 - 15:19:50 PDT)
- [AMBER] translational diffusion coefficient from MSD Kris Feher (Thu Jul 12 2018 - 15:44:36 PDT)
- [AMBER] Reduced GPU Performance Midhun K Madhu (Fri Jul 13 2018 - 03:40:54 PDT)
- [AMBER] Single Point Calculation on trajectory Raimon Fabregat (Fri Jul 13 2018 - 06:12:50 PDT)
- [AMBER] Per-residue energy decomposition by MMPBSA.pl Syeda (Fri Jul 13 2018 - 09:51:05 PDT)
- [AMBER] convert trajectories files in AMBER Chhaya Singh (Fri Jul 13 2018 - 10:31:00 PDT)
- [AMBER] calculating headgroup ion-ion and ion-dipole contacts for lipid bilayers Sally Pias (Fri Jul 13 2018 - 15:14:33 PDT)
- [AMBER] Per-residue energy decomposition by MMPBSA.pl S (Fri Jul 13 2018 - 23:30:40 PDT)
- [AMBER] error in leap prmtop incprd preparation senal dinuka (Sun Jul 15 2018 - 08:10:59 PDT)
- [AMBER] Determination of pmf, diffuse, permeability and resistance in case of lipid molecule? zmatovic.kg.ac.rs (Mon Jul 16 2018 - 02:33:26 PDT)
- [AMBER] Distance between two different solvent mask MOHD HOMAIDUR RAHMAN (Mon Jul 16 2018 - 03:23:53 PDT)
- [AMBER] CUDA and Amber 18 Beale, John (Mon Jul 16 2018 - 05:15:46 PDT)
- [AMBER] Au+++ ion parameter Aashish Bhatt (Tue Jul 17 2018 - 04:18:36 PDT)
- Re: [AMBER] AMBER Digest, Vol 2349, Issue 1 Stejskal, Lenka (Tue Jul 17 2018 - 07:46:17 PDT)
- [AMBER] Calcium forcefields Piotr Fajer (Tue Jul 17 2018 - 10:36:55 PDT)
- [AMBER] Problem with NaN and Asteriks Jorge Curima (Tue Jul 17 2018 - 11:59:01 PDT)
- [AMBER] Neural net timestep integration diagram Bill Ross (Tue Jul 17 2018 - 17:54:58 PDT)
- [AMBER] Advice on using GLYCAM parameters senal dinuka (Tue Jul 17 2018 - 23:51:08 PDT)
- [AMBER] Calcium force fields David A Case (Wed Jul 18 2018 - 04:16:10 PDT)
- [AMBER] Amber on GTX 1-5- / 1050 TI ? Gustavo Seabra (Wed Jul 18 2018 - 08:06:12 PDT)
- [AMBER] How to analyse the PCA results? Markowska (Wed Jul 18 2018 - 09:01:59 PDT)
- [AMBER] mask behavior with ions? Kenneth Huang (Wed Jul 18 2018 - 10:37:01 PDT)
- [AMBER] ACE_NME_TLEAP Antonio Carlesso (Wed Jul 18 2018 - 23:38:43 PDT)
- [AMBER] Amber on GTX 1050 / 1050 TI Gustavo Seabra (Thu Jul 19 2018 - 02:26:35 PDT)
- [AMBER] Distance restraint for PMEMD Abir Ganguly (Thu Jul 19 2018 - 05:48:20 PDT)
- [AMBER] Diffusion coefficient from Terachem emanuele falbo (Thu Jul 19 2018 - 07:52:43 PDT)
- [AMBER] CPPTRAJ read different frames Rana Rehan Khalid (Thu Jul 19 2018 - 10:08:23 PDT)
- [AMBER] Amber targeted MD restraintmask 李耀 (Thu Jul 19 2018 - 19:57:33 PDT)
- [AMBER] Arsenous acid (H3AsO3) parameterization Zuo, Zhicheng (Thu Jul 19 2018 - 21:25:32 PDT)
- [AMBER] amber test run ilhan.yavuz (Fri Jul 20 2018 - 05:59:53 PDT)
- [AMBER] Papers that use RPMD in AMBER Rodrigo Pérez Cossio (Fri Jul 20 2018 - 06:08:16 PDT)
- Re: [AMBER] Is Amber18 compatible with GCC-7.x? Mirza Ahmed Hammad (Fri Jul 20 2018 - 23:59:29 PDT)
- [AMBER] partial molar volume of hypothetical protein molecule without atomic charges Leena Aggarwal (Sat Jul 21 2018 - 02:45:51 PDT)
- [AMBER] error in antechamber Andrew Bostick (Sat Jul 21 2018 - 13:15:41 PDT)
- [AMBER] Question about implicit solvation: DNA-linker conjugate Supriyo Bhattacharya (Sun Jul 22 2018 - 11:30:07 PDT)
- [AMBER] Amber targeted MD variables 李耀 (Mon Jul 23 2018 - 02:57:44 PDT)
- [AMBER] Soft-core alchemical transformation in TI Simon Kit Sang Chu (Mon Jul 23 2018 - 08:11:35 PDT)
- Re: [AMBER] trajout last x frames cpptraj Daniel Roe (Mon Jul 23 2018 - 10:34:57 PDT)
- [AMBER] LJEDIT syntax Matias Machado (Mon Jul 23 2018 - 11:15:50 PDT)
- [AMBER] analyze force on selected atoms James Kress (Mon Jul 23 2018 - 12:22:20 PDT)
- [AMBER] Query regarding multiplication of LJ parameters by a constant in topology file using parmed Leena Aggarwal (Tue Jul 24 2018 - 06:06:56 PDT)
- Re: [AMBER] Is Amber18 compatible with GCC-7.x Nikolay N. Kuzmich (Tue Jul 24 2018 - 14:41:19 PDT)
- [AMBER] problem preparing n-terminus with tleap (?) Julia Belk (Tue Jul 24 2018 - 18:32:26 PDT)
- [AMBER] Problem in chamber Suzan Bose (Tue Jul 24 2018 - 21:10:45 PDT)
- [AMBER] Reading grid data from standard datafile I Lőrincz (Wed Jul 25 2018 - 04:55:09 PDT)
- [AMBER] MCBP force constants Seibold, Steve Allan (Wed Jul 25 2018 - 10:23:02 PDT)
- [AMBER] Extract Force from MDCRD/DCD trj Lod King (Wed Jul 25 2018 - 17:50:09 PDT)
- [AMBER] The instructions of the .out file Zhonghua Xia (Fri Jul 27 2018 - 03:48:05 PDT)
- [AMBER] The instructions of the .out file Zhonghua Xia (Fri Jul 27 2018 - 03:57:25 PDT)
- [AMBER] The instructions of the .out file Zhonghua Xia (Fri Jul 27 2018 - 04:04:35 PDT)
- [AMBER] The right syntax for creating the given mask using logical operators - Not all arguments handled Marek Maly (Fri Jul 27 2018 - 06:18:27 PDT)
- [AMBER] CPPTRAJ contacts and nativecontacts PAQUET Amaury (Fri Jul 27 2018 - 07:16:35 PDT)
- [AMBER] Thermodyncamic Integration (TI) emanuele falbo (Fri Jul 27 2018 - 08:45:14 PDT)
- [AMBER] very slow implicit simulation on GPU!!! Parviz Seifpanahi Shabane (Fri Jul 27 2018 - 13:15:26 PDT)
- [AMBER] Possible bug on addLJType command of Parmed Matias Machado (Fri Jul 27 2018 - 20:20:19 PDT)
- [AMBER] Inquries about Non-periodic PMF profile Meng Wu (Sat Jul 28 2018 - 07:26:37 PDT)
- [AMBER] Amber targeted MD tgtmdfrc 李耀 (Sat Jul 28 2018 - 09:59:25 PDT)
- [AMBER] Gaff vs Gaff2 when using antechamber to generate charges Yuliana Bosken (Sat Jul 28 2018 - 15:31:48 PDT)
- [AMBER] Amber targeted MD tgtmdfrc 李耀 (Sat Jul 28 2018 - 22:29:19 PDT)
- [AMBER] Amber ff for oniom method roja rahmani (Sun Jul 29 2018 - 21:15:22 PDT)
- [AMBER] SANDER BOMB in subroutine qm2_extern_get_qm_forces Devashish_Das (Mon Jul 30 2018 - 01:07:32 PDT)
- [AMBER] Cpptraj PCA analysis - correlation between PCs? Markowska (Tue Jul 31 2018 - 01:28:55 PDT)
- [AMBER] QM/MM link atoms emanuele falbo (Tue Jul 31 2018 - 04:09:10 PDT)
- [AMBER] TIP4P inputs and tests Brian Radak (Tue Jul 31 2018 - 07:13:04 PDT)
- [AMBER] Running a small minimization with amber 16 package Debarati DasGupta (Tue Jul 31 2018 - 09:34:26 PDT)
- [AMBER] FMNH2 parameters Maximilian Ebert (Tue Jul 31 2018 - 20:31:28 PDT)
- Last message date: Tue Jul 31 2018 - 21:00:02 PDT
- Archived on: Mon Nov 25 2024 - 05:55:35 PST
