Re: Using 4-site water model in NAMD

From: Nassar, Omneya (omnassar_at_UTMB.EDU)
Date: Sun Sep 16 2018 - 22:05:37 CDT

Sorry I just saw the link you left at the bottom. Please ignore the previous email.

Thank you,

Omneya

On Sep 16, 2018, at 10:04 PM, Nassar, Omneya <omnassar_at_UTMB.EDU<mailto:omnassar_at_UTMB.EDU>> wrote:

Hello Haohao,

Can you send the error message that you receive as well as the NAMD input file you are using?

Thank you,

Omneya

On Sep 16, 2018, at 8:11 PM, Haohao Fu <fhh2626_at_gmail.com<mailto:fhh2626_at_gmail.com>> wrote:

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Dear All,

I'm trying to equilibrate a TIP4P water box using NAMD. However, when I submit such job, the NAMD process will stop in 10 timesteps. I suspect that there are something wrong in my psf file, but I cannot figure out where the problem is.

I used the official version of "toppar_water_ions_tip4p.str" in http://mackerell.umaryland.edu/charmm_ff.shtml%7C0%7C636727435076290863&sdata=%2BIyrWKzEcgz6JlAOzDM%2BnfxYksviVLRMIsuWFm6rs9A%3D&reserved=0> and tried both NAMD 2.12 and 2.13b1. The "waterModel" option is set to "tip4". All the files used can be download in https://drive.google.com/open?id=1HCZLPU1uHnPplwMC_8CAqX7LBsaenE4S9c2%7C7bef256d85db4526a72d31aea2546852%7C0%7C0%7C636727435076290863&sdata=CqcaLfh%2BdJGpATGZZMn161SExaGULgvB0Dt6fR2FU3s%3D&reserved=0>.

Could anyone help me out? Thanks!

Best,
Haohao

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