Hi Yinglong,
Thanks for your reply. Below is my gamd input script and it keeps crashing
(after 80% steps) without errors on the HPC. Does ligGAMD require ntf=1?
Thank you in advance for your help.
&cntrl
imin = 0, irest = 1,
nstlim = 26000000, dt = 0.002,
ntc=2,ntf=1,ig=-1,iwrap=1,
cut=12.0, ntb=2, ntp=1, taup=2.0,
ntpr=2500, ntwx=2500,ntwr=2500,
ntt=3, gamma_ln=1.0,
temp0=300.0,
igamd = 11, irest_gamd = 0,
ntcmd = 1000000, nteb = 25000000, ntave = 200000,
ntcmdprep = 200000, ntebprep = 800000,
sigma0P = 4.0, sigma0D = 6.0, iEP = 2, iED=1,
icfe = 1, ifsc = 1, gti_cpu_output = 0, gti_add_sc = 1,
timask1 = ':476-479', scmask1 = ':476-479', timask2 = '', scmask2 = '',
ibblig = 1, nlig = 4, atom_p = 200, atom_l = 7509, dblig = 3.7,
&end
On Fri, 23 Oct 2020 at 13:10, Miao, Yinglong <miao.ku.edu> wrote:
> Hi Neha,
>
> You need to put atom mask for *only the first ligand* for timask1 and
> scmask1. You can find more details in the Amber20 manual and also here:
> http://miao.compbio.ku.edu/GaMD/manual.html.
>
> Best,
> Yinglong
>
> Yinglong Miao, Ph.D.
> Assistant Professor
> Center for Computational Biology and
> Department of Molecular Biosciences
> Department of Medicinal Chemistry (courtesy)
> University of Kansas
> Tel: 1-785-864-8298
> http://miao.compbio.ku.edu
>
> On Oct 22, 2020, at 5:30 PM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
>
> Hi List,
>
> I am going through the GaMD manual and tutorial. I have 4 ligands the
> system.
> In the input script below, timask1 refers to ligand1. Do we have to put
> individual timask for remaining ligands in the systems or only include for
> first ligand?
>
>
>
> *timask1 = ':225', scmask1 = ':225', timask2 = '', scmask2 = '', *
>
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Vice Chancellor's Research Fellow,
> Queensland University of Technology,
> 2 George Street, Brisbane, QLD 4000
> Australia
> LinkedIn
> Research Gate
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--
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
LinkedIn
Research Gate
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Received on Sun Oct 25 2020 - 17:30:03 PDT
