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-- Regards, Dr. Vaibhav A. Dixit, Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK. AND Assistant Professor, Department of Pharmacy, ????????????????????????????????????????????? Birla Institute of Technology and Sciences Pilani (BITS-Pilani), VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031. India. Phone No. +91 1596 255652, Mob. No. +91-7709129400, Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/ ORCID ID: https://orcid.org/0000-0003-4015-2941 http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra P Please consider the environment before printing this e-mail ------------------------------ Message: 6 Date: Sat, 17 Apr 2021 11:59:56 -0400 From: Ramin Mehrani <raminmehrani88.gmail.com> Subject: [AMBER] Umbrella sampling on Amber 18 vs Amber 20 To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAEnbn5TQ0WJ1pj8-H+2wd6fC7-4jLeUDQvTtPJo7qotEHDg-aw.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Hello, I am running an umbrella sampling simulation using "colvar" namelist and COM_DISTANCE as the reaction coordinate to keep the distance constant between two chains of my protein. I notice that this method only works when I am using amber/18 and when I ran the exact same simulation(same input, initial configurations and ...) on Amber/20 the protein will get unfolded in an obviously wrong configuration and also the constrain distance is not satisfied. I should also mention that in both cases I am using GPU. I was wondering if there is anything that I need to change in Amber/20 to get similar result or the Amber/20 is not good for running umbrella sampling. Thanks, Ramin ------------------------------ Message: 7 Date: Sat, 17 Apr 2021 12:47:41 -0400 From: David A Case <david.case.rutgers.edu> Subject: Re: [AMBER] Umbrella sampling on Amber 18 vs Amber 20 To: AMBER Mailing List <amber.ambermd.org> Message-ID: <20210417164741.pfohcowfyoy2wz3r.sas1065303ec708.rad.rutgers.edu> Content-Type: text/plain; charset=us-ascii; format=flowed On Sat, Apr 17, 2021, Ramin Mehrani wrote: > >I am running an umbrella sampling simulation using "colvar" namelist >and COM_DISTANCE as the reaction coordinate to keep the distance constant >between two chains of my protein. I notice that this method only works when >I am using amber/18 and when I ran the exact same simulation(same input, >initial configurations and ...) on Amber/20 the protein will get unfolded >in an obviously wrong configuration and also the constrain distance is not >satisfied. I should also mention that in both cases I am using GPU. I was >wondering if there is anything that I need to change in Amber/20 to get >similar result or the Amber/20 is not good for running umbrella sampling. Can you provide a small example that illustrates the problem? ...thanks...dac ------------------------------ Message: 8 Date: Sat, 17 Apr 2021 13:20:32 -0400 From: Ramin Mehrani <raminmehrani88.gmail.com> Subject: Re: [AMBER] Umbrella sampling on Amber 18 vs Amber 20 To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAEnbn5RbBbs5xcAEgAm-u2sVXC-2RAC3EjEctk5tMWWzRq-uoA.mail.gmail.com> Content-Type: text/plain; charset="utf-8" [image: Amber20.PNG] [image: Amber18.PNG] Hello, Thank you for your response, below are the snapshots of two different results that I am getting on Amber/18 and Amber/20 while I am using the exact same two attached input files. Please let me know if you need more specific information. Thanks, Ramin input file1: &cntrl imin=0, ntx=1, irest=0, pres0=1.0, taup=1.0, temp0=310.0, tempi=310.0, nstlim=1000000, dt=0.002, ntf=2, ntc=2, ntpr=50000, ntwx=50000, ntwr=50000, cut=10.0, ntb=2, ntp=1, ntt=3, gamma_ln=3.0, ig=-1, iwrap=1, infe = 1, / &pmd output_file = 'pmd.txt' output_freq = 10 cv_file = 'cv.in' / &ewald skinnb=3.0, / input file2(cv.in) cv_file &colvar ! first cv_type = 'COM_DISTANCE' cv_ni =3652 cv_i 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anchor_position=-99.0,32.0,32.0,99.0 anchor_strength = 8,8 / On Sat, Apr 17, 2021 at 12:47 PM David A Case <david.case.rutgers.edu> wrote: > On Sat, Apr 17, 2021, Ramin Mehrani wrote: > > > >I am running an umbrella sampling simulation using "colvar" namelist > >and COM_DISTANCE as the reaction coordinate to keep the distance constant > >between two chains of my protein. I notice that this method only works > when > >I am using amber/18 and when I ran the exact same simulation(same input, > >initial configurations and ...) on Amber/20 the protein will get unfolded > >in an obviously wrong configuration and also the constrain distance is not > >satisfied. I should also mention that in both cases I am using GPU. I was > >wondering if there is anything that I need to change in Amber/20 to get > >similar result or the Amber/20 is not good for running umbrella sampling. > > Can you provide a small example that illustrates the problem? > > ...thanks...dac > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > -------------- next part -------------- A non-text attachment was scrubbed... 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