Re: [gmx-users] InflateGRO and pentamer protein simulation

Dear Xi Zhao, For inserting protein into membrane you might like to try use g_membed (link http://wwwuser.gwdg.de/~ggroenh/membed.html) This is not strictly (yet) a gromacs package, but it can be very easily be complied and used per instructions of the authors. Technically, the package 'compr

[gmx-users] problem with NVE ensemble simulation with Martini lipid

Hi, I am having a problem with running a NVE ( micro-canonical) ensemble using a system of 128 Martini DPPC lipids. I started the simulation with a 128 lipid bilayer with Martini water which was pre-equilibrated in NPT ensemble ( using berendsen temperature coupling at 325 K( separate coupl

Re: [gmx-users] InflateGRO and pentamer protein simulation

Dear sir: Thank you for your help! --- 10年4月11日，周日, shaya...@post.tau.ac.il 写道： 发件人: shaya...@post.tau.ac.il 主题: Re: [gmx-users] InflateGRO and pentamer protein simulation 收件人: jalem...@vt.edu, "Discussion list for GROMACS users" 日期: 2010年4月11日,周日,下午10:01 Dear Xi Zhao, For inserting p

[gmx-users] how to make ice crystal by TIP4P, TIP5P water model

Hi gmx users, Online available ice.pdb has following contents. I think it is made for SPC water model. How can I make ice structure for TIP4P, TIP5P water model? Thanks, HEADERA beautiful Ice Ih crystal REMARKGenerated by mkice with the following options: REMARKnx = 5, ny

Re: [gmx-users] problem with NVE ensemble simulation with Martini lipid

On 12/04/2010 5:01 AM, Sanku M wrote: Hi, I am having a problem with running a NVE ( micro-canonical) ensemble using a system of 128 Martini DPPC lipids. I started the simulation with a 128 lipid bilayer with Martini water which was pre-equilibrated in NPT ensemble ( using berendsen temperature c

Re: [gmx-users] Lateral pressure profile in membrane simulations

Dear users, I am attempting to perform 3D pressure tensor calculation on well-converged all-atom lipid bilayer. I am using modified gromacs and -rerun option and analyze the output with the tools that is provided on Martini website. I had following question: I have a production trajectory fro

[gmx-users] isntall problem of ngmx

 Hello, I have done the ./configure --without-X,why it still would compile the ngmx? I had posted to you that it would make errores  if compiled the ngmx. the errores are like this : In file included from ngmx.c:50: Xstuff.h:48:22: error: X11/Xlib.h: No such file or directory Xstuff.h:49:23: erro

Re: [gmx-users] isntall problem of ngmx

On 12/04/2010 1:38 PM, kecy...@sina.com wrote: Hello, I have done the ./configure --without-X,why it still would compile the ngmx? I had posted to you that it would make errores if compiled the ngmx. the errores are like this : Dunno, maybe it is --disable-X. Please post your actual configure l

Re: [gmx-users] isntall problem of ngmx

You don't have the X library headers installed. 2010/4/11 > Hello, I have done the ./configure --without-X,why it still would compile > the ngmx? I had posted to you that it would make errores if compiled the > ngmx. the errores are like this : > > *In file included from ngmx.c:50:* > > *Xstuf