[gmx-users] finite element methods

Dear GROMACS users, could you please answer the following questions: 1.Is it possible to dock molecules with finite element methods? 2.Can gromacs modules be used for such methods? 3.Does it give time advantage? 4.Can it be solved with a system of linear equations? Thank you in advance.

[gmx-users] *.itp files

Dear Gromacs users, I try to use Gromacs at the step: pdb2gmx -f C:\Soft\Gromacs\Input\formaldehyde.pdb -o outputName.gro -p outputName.top pdb2gmx -f C:\Soft\Gromacs\Input\cyanide.pdb -o outputName.gro -p outputName.top How can I get formaldehyde.itp and cyanide.itp if I have

Re: [gmx-users] water can't freeze

Send me please your files, I would like to have a look at them Alex--- On Fri, 4/18/08, Wei, Xiupeng [EMAIL PROTECTED] wrote: From: Wei, Xiupeng [EMAIL PROTECTED]Subject: [gmx-users] water can't freezeTo: "gmx-users@gromacs.org" gmx-users@gromacs.orgDate: Friday, April 18, 2008, 8:41 PMHi gmx

[gmx-users] Covalent bonds breaking formation

Dear Gromacs users, What software instead of gromacs can I use to treat chemical reactions properly. (See Chapter 1 page 4 of manual-3.3.pdf) What options in gromacs should I use to break and form covalent bonds. (Examples, programs, etc) Thank you in advance.   Alexander

Re: [gmx-users] Announcing: Gromacs 4.0, release candidate 1

What compiler should I use on Windows? Thank you in advance. --- On Sun, 9/21/08, Erik Lindahl [EMAIL PROTECTED] wrote: From: Erik Lindahl [EMAIL PROTECTED] Subject: [gmx-users] Announcing: Gromacs 4.0, release candidate 1 To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sunday,

[gmx-users] pdb files

Dear Gromacs users, Could you please help me to find pdb files for glyceric acid esters cyanamide phosphatidylcholine glyceroyl thioesters tetrose polyglyceric acid hemiacetal Thank you in advance - Moody friends. Drama queens. Your life?

Re: [gmx-users] pdb files

Dear Mark Abraham Thank you very much for your help. Could you please help me to find such a not free molecule building program. Maybe it will be useful anyway somehow. Thank you in advance. Mark Abraham [EMAIL PROTECTED] wrote: Sagittarius wrote: Dear Gromacs users, Could you

[gmx-users] Residue 'UNK' not found in residue topology database

Dear Gromacs users, Could you please help me to find out what the problem is. I use command pdb2gmx -f C:\Soft\Gromacs\Input\formaldehyde.pdb -o outputName.gro -p outputName.top formaldehyde.pdb looks like this: COMPNDUNNAMED

[gmx-users] Residue abbreviation list with explanations

Dear Gromacs users, Could you please help me to find a Residue abbreviation list web site. I need to replace UNK below with something meaningful. formaldehyde.pdb looks like this: COMPNDUNNAMED REMARK 1 PDB to MMOD

RE: [gmx-users] Residue abbreviation list with explanations

And what is my current issue is? What should I replace the residue name with? Dallas B. Warren [EMAIL PROTECTED] wrote:Could you please help me to find a Residue abbreviation list web site. If you want to find out what people are calling a particular molecule or residue, best place to

Re: [gmx-users] Residue abbreviation list with explanations

And this is what I found there: see if there is a different name being used for the residue in the residue database and rename as appropriate, Mark Abraham [EMAIL PROTECTED] wrote: Sagittarius wrote: Dear Gromacs users, Could you please help me to find a Residue abbreviation list

[gmx-users] Examples

Dear Gromacs users, Could you please help me to find any examples of 2 component simple reactions with all the preliminary calculations and further data files for simulations on Gromacs. Thank you in advance Alex - Take the Internet to

Re: [gmx-users] Examples

It is more disturbing for you with specific questions. If I have examples it would be much easier for everyone. David van der Spoel [EMAIL PROTECTED] wrote: Sagittarius wrote: Already started and there are no examples there If you want specific help, ask a specific question. Otherwise

[gmx-users] OPLS parametes

Hi, does anyone know if there is an OPLS topology for cyanide cyanamide formaldehyde glyceraldehyde glycericAcidEster glycerol glyceroylThioester glycolaldehyde hemiacetal tetrose around. Thanks a lot in advance - Don't let your

[gmx-users] ngmx error messages

Dear Gromacs users, I am trying to compile ngmx part of Gromacs (I assume grphics). Visual studio linking gives error messages including: xutil.obj : error LNK2001: unresolved external symbol _XLookupString xutil.obj : error LNK2001: unresolved external symbol _XChangeWindowAttributes

Re: [gmx-users] ngmx error messages

I already have some kind of cygwin. Could you please provide me with more details on install cygwin with some kind of X server Thank you in advance David van der Spoel [EMAIL PROTECTED] wrote: Sagittarius wrote: Dear Gromacs users, I am trying to compile ngmx part of Gromacs (I assume

Re: [gmx-users] ngmx error messages

Thank you very much Justin A. Lemkul [EMAIL PROTECTED] wrote: When you run the setup.exe for Cygwin, install the X11 package. Quoting David van der Spoel : Sagittarius wrote: I already have some kind of cygwin. Could you please provide me with more details on install cygwin with some