[gmx-users] Re: gmx-users Digest, Vol 38, Issue 29

>It's hard to work out your problem, but it sounds like you haven't read >manual section 3.2 yet. Please do so, and get back to us. > >Mark Thanks Mark! I will check manual. I am really sorry for bothering! BEST REGARDS ___ gmx-users mailing list

[gmx-users] question about PBC and link cell based cutoff method

Dear GMX community! I have question about PBC and link cell based cutoff method. (1) for example one water molecule,if only H atom of one water molecule move out of box, however, O atom are still in the box. does this H atom will need to be image back to the box through PBC,or just ignore it unt

[gmx-users] Re: question about dihedral angle in *.itp file

-- > >Message: 2 >Date: Wed, 03 Jan 2007 08:51:47 +0100 >From: David van der Spoel <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] question about dihedral angle in *.itp file >To: Discussion list for GROMACS users >Message-ID: <[EMAIL PROTECTED]> >

[gmx-users] question about dihedral angle in *.itp file

Dear GMX community! I have a question about dihedral angle in *.itp file. question 1: why several torsional dihedral angles with different parameters can be defined on the same set of atoms i, j, k, and l. question 2: how do we get multiplicity m if we want to make some parameter for some tors

[gmx-users] how to calculate the area of per lipid in membrane

Dear gmx community! Could anyone help me how to perform the analysis of after MEMBRANE simulation in NPT condition. because there is a protein inserted in the membrane, it is difficult for me to calculate the area of per lipid directly. what kinds of program can do such work. Thank you very muc

[gmx-users] ForceField for SDPC(sphingomyelin)

Dear Gmx community I am new to memberane simulation. i want to simulate membrane, which consists DPPC and SDPC(Sphingomyelin). luckily, i got the force field and coordinates for DPPC (dppc.itp,dppc.pdb) from Doctor Peter Tieleman'websites.however,i cannot find the force field and coordinates for

[gmx-users] total energy of system is positive,MD normal ?

Dear all! My Simulation was done in decane and dmso. during analysis(g_energy), i find the energy of the whole system is positive not negative.however, fluctuation of temperature ,pressure and total energy is normal. Could anyone help me to figure out whether this MD is normal or not! Thank you