Re: [gmx-users] high-temperature MD

> Sent: 06 October 2016 09:34:49 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] high-temperature MD > > On 10/6/16 8:54 AM, OuyangYanhua wrote: >> Dear Justin, >>> >> I had run a 300K-MD, now I want to run a high-temperature(380K) MD to >> compare with

Re: [gmx-users] high-temperature MD

Dear Justin, > I had run a 300K-MD, now I want to run a high-temperature(380K) MD to compare with the 300K-MD. The 300K is first equilibrated at NVT, then at NPT and production MD at NPT. So I want to know the high-temperature(380K) MD should run the same as the 300k, which means the 380k is

Re: [gmx-users] minimum distance between the protein and its mirror image

The minimum protein-image distance is less than the value 2.0nm, such as t around 1.6nm above. Does it mean my simulation is failed in the box size set? > 在 2016年8月29日，下午8:58，Justin Lemkul 写道： > > > > On 8/29/16 5:02 AM, YanhuaOuyang wrote: >> Hi, >> I am running a REMD of

[gmx-users] Failed to lock: pre.log

Hi, I am running a 100ns-REMD with 50 replicas. when continuing the REMD by appending to the old output files, such error happened: "Fatal error:Failed to lock: md1.log. Already running simulation?” Then I had a test of 5 replicas. I limit the run time for 10 minutes for every

Re: [gmx-users] converting the frcmod file and off file to gromacs

rk Abraham <mark.j.abra...@gmail.com>: > >> Hi, >> >> It sounds like what you want to look for is the documentation for those >> file formats. >> >> Mark >> >> On Sun, 19 Jun 2016 10:05 OuyangYanhua <15901283...@163.com> wrote: >>

Re: [gmx-users] converting the frcmod file and off file to gromacs

Thank you for your recommend. > 在 2016年6月20日，下午10:22，Mark Abraham <mark.j.abra...@gmail.com> 写道： > > Hi, > > It sounds like what you want to look for is the documentation for those > file formats. > > Mark > > On Sun, 19 Jun 2016 10:05 OuyangYanhua <159

Re: [gmx-users] Average exchange probability when extending REMD

? > 在 2016年6月15日，下午9:34，Mark Abraham <mark.j.abra...@gmail.com> 写道： > > Hi, > > That's never been implemented, unfortunately. > > Mark > > On Wed, Jun 15, 2016 at 3:25 PM OuyangYanhua <15901283...@163.com> wrote: > >> Hi, >> I extende

[gmx-users] Average exchange probability when extending REMD

Hi, I extended the REMD of a protein in a explicit water and append the data to the old ones and it appended. However, at the end of the .log files, the replica exchange statistics section only contains the data of extended time, it did not combine the former statistics and the extended