GaMD with 4 fs and HMR

[groponp]

Dear,

I want do ask if is possible perform GaMD with HMR (4fs) in NAMD2 o NAMD3.

best.

[MiaoLab20]

We test using 4fs with GaMD in Amber, which runs fine, but not yet with NAMD. They should be compatible though. Yinglong

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________________________________ From: Ropón-Palacios G. ***@***.***> Sent: Monday, February 19, 2024 3:47:42 PM To: MiaoLab20/pyreweighting ***@***.***> Cc: Subscribed ***@***.***> Subject: [MiaoLab20/pyreweighting] GaMD with 4 fs and HMR (Issue #4) You don't often get email from ***@***.*** Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Dear, I want do ask if is possible perform GaMD with HMR (4fs) in NAMD2 o NAMD3. best. — Reply to this email directly, view it on GitHub<#4>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ARJGPFRCZLIE6LRDASZVBYDYUO265AVCNFSM6AAAAABDQBKNX6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGE2DGMJSGIYDGOI>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[groponp]

Thanks Prof for your answer. What parameters (ex, total energy, temperature, etc)I would can check, to be sure that the system is stable?.

[MiaoLab20]

We have normally run simulations on model alanine dipeptide, calculate its free energy profiles, and compare results between GaMD (4fs this case) and long-time conventional MD to make sure the simulations are accurate. Yinglong On Feb 21, 2024, at 6:45 AM, Ropón-Palacios G. ***@***.***> wrote: You don't often get email from ***@***.*** Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Thanks Prof for your answer. What parameters (ex, total energy, temperature, etc)I would can check, to be sure that the system is stable?. — Reply to this email directly, view it on GitHub<#4 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ARJGPFWSATUJNMDLJ53DQG3YUXM6JAVCNFSM6AAAAABDQBKNX6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNJWGQ3TKMZZGU>. You are receiving this because you commented.Message ID: ***@***.***>

[groponp]

How much long have that be the GaMD and conventional simulation?

[MiaoLab20]

For alanine dipeptide, 30-60 ns GaMD and 1000 ns conventional MD will be good. Longer runs would be needed for larger systems. Yinglong On Feb 21, 2024, at 7:49 AM, Ropón-Palacios G. ***@***.***> wrote: You don't often get email from ***@***.*** Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> How much long have that be the simulation? — Reply to this email directly, view it on GitHub<#4 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ARJGPFTPMTDZEOOSHT4CB53YUXUNDAVCNFSM6AAAAABDQBKNX6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNJWGU4DEOBSGA>. You are receiving this because you commented.Message ID: ***@***.***>