Re: [gmx-users] Re: The molecule size (jiqing)

  》Has this force field been demonstrated to be effective >for this sort of>simulation? If not, maybe you've begun to demonstrate >that it isn't?>Mark   Yes , you are quite right. In GMX manual 3.2, at the end of chapter 4, it was said that gromos96 is not, however, recommended for

[gmx-users] Re: The molecule size (jiqing)

Hi:>  > >  > Two melt models were built for polyethylene (PE) and>  > polyvinylmethylether (PVME) melt with PBC condition .>  > >  > The density of both melt model agree with experimenal value well.But>  > when one check the radius of gyration (Rg) of them, both of them were>  > too

Re: [gmx-users] The molecule size

> Hi:>  > Two melt models were built for polyethylene (PE) and > polyvinylmethylether (PVME) melt with PBC condition .>  > The density of both melt model agree with experimenal value well.But > when one check the radius of gyration (Rg) of them, both of them were > too small to acce

[gmx-users] The molecule size

Hi:   Two melt models were built for polyethylene (PE) and polyvinylmethylether (PVME) melt with PBC condition .   The density of both melt model agree with experimenal value well.But when one check the radius of gyration (Rg) of them, both of them were too small to accept as foll

[gmx-users] Tip5p with gromos 96, error atom has mass 0

Hi all: I built a topol file for tip5p water accordint to tip5p.itp which is designed for OPLS.But when i used grompp to built a tpr file, three errors came even the system just have one tip5p water.   The error is :   ERROR 1 [file "topol.top", line 10]:   atom OW has mass 0

[gmx-users] tip4p or 5p

I want to build a water cell with 4p or 5p.How can i realized it? May be after include *.itp in current top, something need to be modified? It was said that 4p or 5p  need OPLS together.   How can i used it in GROMOS 96   *Ji Qing

[gmx-users] The water model with tip5p in gromos96

Hi everyone: I found that in tip5p.itp, there is a note tell user to use tip5p model with opls force field.   But what i really want to use is the gromos96. How can i include tip5p model?   Thanks a lot *Ji QingInstitute of Chemistry

[gmx-users] Re: MD run end abnormally

 Problem has been fixed!   Just add the 'nohup' in front of 'mdrun'       *Ji Qing（吉青）Institute of Chemistry, Chinese Academy of Sciences（中科院化学所）Tel: 0086-10-62562894  ，82618423*  

[gmx-users] MD run end abnormally

 Hi :Mark, thanks for your advice. But i only use the single-processor.And the enviourment is RedHat 9.0 with gromacs 3.3.1.     And if i just use mdrun -v, the process goes well. if i use mdrun -v >& output&, the problem will occur.  what is other problem of this error Date: Sun,

[gmx-users] MD run end abnormally

 Hi :Mark, thanks for your advice. But i only use the single-processor.And the enviourment is RedHat 9.0 with gromacs 3.3.1. what is other problem of this error Date: Sun, 2 Jul 2006 15:17:53 +1000 (EST)From: "Mark Abraham" <[EMAIL PROTECTED]>Subject: Re: [gmx-users] MD run end abno

[gmx-users] MD run end abnormally more detailed info

Hi : Mark, thanks for your advice.   But i only use the single-processor.And the enviourment is RedHat 9.0 with gromacs 3.3.1.   what is other problem of this error   Date: Sun, 2 Jul 2006 15:17:53 +1000 (EST)From: "Mark Abraham" <[EMAIL PROTECTED]>Subject: Re: [gmx-users] MD run

[gmx-users] MD run end abnormally

Hi:   I install GMX FFTW MPI in my own folders. And then i used a begin structure which performed well at other computers to test the GMX programme.   What is strange to me is that the job can run well at begginning time but after a while the CPU was not still busy, and the output

[gmx-users] re:grompp error:Invalid order for directive defaults

  It may caused by the difference in file type of top . Did you change your top file under win system. If yes , you should change it to unix type. Also you can check the property of top file.   祝   好   *Ji Qing（吉青）Institute of Chem

[gmx-users] compile GMX source code by VC 6.0

    Hi: I tried to compile GMX source code by VC 6.0.   I found the main function of MD simulation is in mdrun.c. And then i compiled it as main file.   But some varier type my compiler can not find . Such as :  LONG; TCHAR; BSTR;  BOOL; DATE;  How can i fix it !   thanks a