Re: [gmx-users] how are you

Hi, Dr. Liang Please use PRODRG server. http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ or you can write some script to convert Material studio pdb file to PDB bank format. Thanks. On 10/31/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: > > Sir: > How are you! I am a new user of gmx.At f

[gmx-users] Suggestion needed for new workstation

Hi, everybody. I want to buy a new workstation for MD simulation. I think the Mac Pro from Apple is really nice. The configuration: *Two 3.0GHz Quad-Core Intel Xeon * *8GB (4 x 2GB) * *500GB 7200-rpm Serial ATA 3Gb/s with price: *$6,225.00 Any suggestions or comments? Thanks in advance. * *-- Si

[gmx-users] About Temperature Gradient

Hi, I need a temperature gradient during the simulation. That means I need put a heating source on one end of the box. Can Gromacs do it? Thanks in advance. -- Sincerely yours, James Jianzhang ___ gmx-users mailing listgmx-users@gromacs.org http://

Re: [gmx-users] mdp file help

You can get a typical mdp file from some tutorials. By the way, I think the topology is wrong. Thanks. On 7/18/07, Christopher Stiles <[EMAIL PROTECTED]> wrote: I am trying to simulate a single wall CNT in a box filled with water for about 500 ps and 300K just to start and I am having trouble

Re: [gmx-users] Problems about sigma & epsilon to C6 & C12

ved. Finally I realized that my calculation is wrong. > Thank you so much! > > On 7/15/07, james zhang <[EMAIL PROTECTED]> wrote: > > > > From equation 5.3 page 88, I think rule 1 and 3 are equivalent if you > > convert the parameters. > > I am sorry. What&#

Re: [gmx-users] Problems about sigma & epsilon to C6 & C12 LJ-parameters conversion

My problem has solved. Finally I realized that my calculation is wrong. Thank you so much! On 7/15/07, james zhang <[EMAIL PROTECTED]> wrote: From equation 5.3 page 88, I think rule 1 and 3 are equivalent if you convert the parameters. I am sorry. What's the different between rule

Re: [gmx-users] Problems about sigma & epsilon to C6 & C12 LJ-parameters conversion

alent. I am confused. Can I convert sigma/epsilon to C6/C12 if I want to use gmx force field instead of OPLS ? Thanks. On 7/15/07, David van der Spoel <[EMAIL PROTECTED]> wrote: james zhang wrote: > I used rule 3 for ffopls rule 1 for ffgmx. > please read the manual.these combinat

Re: [gmx-users] Problems about sigma & epsilon to C6 & C12 LJ-parameters conversion

On 7/15/07, David van der Spoel <[EMAIL PROTECTED]> wrote: james zhang wrote: > I did convert the parameters according to Manual chapter 4.11 and 5.3.3. > I used C6=4*epsilon*sigma^6 and C12=4*epsilon*sigma^12 formula. > If my conversion is right, then where is wrong? how abo

Re: [gmx-users] Problems about sigma & epsilon to C6 & C12 LJ-parameters conversion

-users/2004-July/011337.html Why did the same system get totally different simulation result when I changed the L-J expressions? Thanks. On 7/15/07, David van der Spoel <[EMAIL PROTECTED]> wrote: james zhang wrote: > Hi, > > I am trying to do some simulation of chloroform sy

[gmx-users] Problems about sigma & epsilon to C6 & C12 LJ-parameters conversion

Hi, I am trying to do some simulation of chloroform system and I need convert sigma & epsilon to C6 & C12 LJ-parameters. I use C6=4*epsilon*sigma^6 and C12=4*epsilon*sigma^12 formula. This is my result [ atomtypes ] ;typemasscharge ptype sigma epsilon CH 12.0110

Re: [gmx-users] pressure scaling more than 1%

ok, Thanks a lot On 10/1/06, David van der Spoel <[EMAIL PROTECTED]> wrote: james zhang wrote:> Hi,>> I try to compress a box at a high pressure, but the box alwasys > collapsed after several steps.>> And I get the error:  /pressure scaling more than 1%/>> How can I g

[gmx-users] pressure scaling more than 1%

Hi,   I try to compress a box at a high pressure, but the box alwasys collapsed after several steps.   And I get the error:  pressure scaling more than 1%   How can I get over this problem.   Thanks in advance. -- Sincerely yours,James jianzhangDepartment of Mechanical and Chemical Engineering Nort

[gmx-users] running CPMD with GROMACS interface in SGI irix 6.5

Hi   I got some trouble in running CPMD with GROMACS interface in SGI irix 6.5. Thanks in advance   the error is  [PEAK NUMBER  116]   PEAK MEMORY  14169180 =  113.4 MBytes [ALL. NUMBER  116]  TOTAL MEMORY  13983696 =  111.9 MBytes =

[gmx-users] GROMACS 3.3.1 installation on SGI (Irix)

Hi:I have just fixed the following make_edi.c errors, by changing the code to:{ "-linfix", FALSE, etSTR, {&evSelections[evLINFIX]},{ "-linacc", FALSE, etSTR, {&evSelections[evLINACC]}, { "-radfix", FALSE, etREAL, {&evSelections[evRADFIX]},And I succeeded to compile and install gromacs 3.3.1.But I s