Re: [gmx-users] Hydrogen bonding

2009-11-17 Thread Justin A. Lemkul
Sarah Witzke wrote: Dear gmx-users, I have done simulations of one small molecule that diffuses into a DMPC membrane. This small molecule contains an alcohol group and is therefore capable of hydrogen bonding to the oxygens of DMPC (phosphate and glycerol region). I have read the manual (se

[gmx-users] Hydrogen bonding

2009-11-17 Thread Sarah Witzke
Dear gmx-users, I have done simulations of one small molecule that diffuses into a DMPC membrane. This small molecule contains an alcohol group and is therefore capable of hydrogen bonding to the oxygens of DMPC (phosphate and glycerol region). I have read the manual (section 8.12 and g_hb

Re: [gmx-users] Tabulated non-bonded potential

2009-11-17 Thread Mark Abraham
ms wrote: Hi, I would like to understand a basic question about the usage of tabulated potential for non-bonded interaction. If I use an arbitrary function and I write a table for it, is the functional shape then applied to *all* my atoms, or can I specify which ones use the tabulated potential

Re: [gmx-users] Decreasing MSD of ligand ?

2009-11-17 Thread Justin A. Lemkul
Chih-Ying Lin wrote: HI MSD = mean square displacement diffusion coefficient = d/dt (MSD) I simulate the protein and ligand system and then calculate the MSD of the ligand. Then, i drew the plot of the time evolution of the MSD. But the the MSD decreases as time for some period. I see not

[gmx-users] Decreasing MSD of ligand ?

2009-11-17 Thread Chih-Ying Lin
HI MSD = mean square displacement diffusion coefficient = d/dt (MSD) I simulate the protein and ligand system and then calculate the MSD of the ligand. Then, i drew the plot of the time evolution of the MSD. But the the MSD decreases as time for some period. I see nothing about my codings. Would yo

[gmx-users] Tabulated non-bonded potential

2009-11-17 Thread ms
Hi, I would like to understand a basic question about the usage of tabulated potential for non-bonded interaction. If I use an arbitrary function and I write a table for it, is the functional shape then applied to *all* my atoms, or can I specify which ones use the tabulated potential -and how? T

RE: [gmx-users] segmentation fault in g_anaeig

2009-11-17 Thread Berk Hess
Hi, The problem that I fixed last week occured after the use of g_covar -mwa with a fit selection that is not the first N atoms of the system. Berk > Date: Tue, 17 Nov 2009 18:03:37 +0100 > Subject: Re: [gmx-users] segmentation fault in g_anaeig > From: tsje...@gmail.com > To: gmx-users@gromacs

Re: [gmx-users] segmentation fault in g_anaeig

2009-11-17 Thread Tsjerk Wassenaar
Hi Nilu, Can you paste the exact commands you entered, and indicate the selections you made? Oh, and can you check the archives to whether this is the same problem that was reported a few weeks ago? Cheers, Tsjerk On Tue, Nov 17, 2009 at 5:53 PM, Nilu Chakrabarti wrote: > I am used to do PC an

[gmx-users] segmentation fault in g_anaeig

2009-11-17 Thread Nilu Chakrabarti
I am used to do PC analysis with g_covar followed by g_anaeig. But recently, I am getting segmentation fault with g_anaeig. The g_covar gives eigenval.xvg, eigenvec.trr and average.pdb. In the next step I use those 3 files to generate - (1) a projection of each individual vectors on the traj using

Re: [gmx-users] pdb2gmx : treat CL as C

2009-11-17 Thread Justin A. Lemkul
Nilesh Dhumal wrote: Tsjerk, When I open di.pdb (output file) in VMD. I see all CL are repalced by C. I can't go to next step. What information do you want more. I checked the format of pdb file again. Its looks dioxin.pdb is ok. After running pdb2gmx, the di.pdb output file don't have any CL

Re: [gmx-users] pdb2gmx : treat CL as C

2009-11-17 Thread Nilesh Dhumal
Tsjerk, When I open di.pdb (output file) in VMD. I see all CL are repalced by C. I can't go to next step. What information do you want more. I checked the format of pdb file again. Its looks dioxin.pdb is ok. After running pdb2gmx, the di.pdb output file don't have any CL atom. Hopes you get me n

Re: [gmx-users] pdb2gmx : treat CL as C

2009-11-17 Thread Tsjerk Wassenaar
Oops, there's an .rtp entry. Shame on me :$ Maybe a good idea though to post the output of pdb2gmx. Cheers, Tsjerk On Tue, Nov 17, 2009 at 3:44 PM, Tsjerk Wassenaar wrote: > Justin, > >> What is the problem?  It looks like you got everything to work, but the .pdb >> file you've posted is misfor

Re: [gmx-users] pdb2gmx : treat CL as C

2009-11-17 Thread Tsjerk Wassenaar
Justin, > What is the problem?  It looks like you got everything to work, but the .pdb > file you've posted is misformatted on the CL lines: > > ATOM     14  C14 PCD     1      -2.372  -1.395   0.000  1.00  0.00 > C > ATOM     15 CL1  PCD     1       5.070   1.618  -0.001  1.00  0.00 >  CL > > Not

Re: [gmx-users] access code for qmmm

2009-11-17 Thread ilona . baldus
Orca is free for example. Apparently, there's an implementation for Gromacs. Please send flowers and chocolate directely to Villa Bosch, where I am working. You find the adress on the internet ;) Quoting Farzad Molani : Hi Ilona, I saw the web adress. unfortunetly we don't have gaussia

Re: [gmx-users] pdb2gmx : treat CL as C

2009-11-17 Thread Justin A. Lemkul
Nilesh Dhumal wrote: here is all information. I attached 2 attachment to my privious mail. It looks 2nd didn't come. Sorry. Here I am giving details. I am using opls force field . I added "PCD" as residue name in aminoacid.dat file. pdb2gmx -f dioxin.pdb -o di.pdb -p di.top -ter i have atta

Re: [gmx-users] pdb2gmx : treat CL as C

2009-11-17 Thread Nilesh Dhumal
here is all information. I attached 2 attachment to my privious mail. It looks 2nd didn't come. Sorry. Here I am giving details. I am using opls force field . I added "PCD" as residue name in aminoacid.dat file. pdb2gmx -f dioxin.pdb -o di.pdb -p di.top -ter i have attached input:dioxin.pdb, ou

Re: [gmx-users] Urea Topology

2009-11-17 Thread Justin A. Lemkul
karan syal wrote: Dear All, I am looking for urea topology* (smith et al) *for gromos 96 force field. I tried searching through user contributions in gromacs site but couldnt find it. Is it possible for anyone who has already used it to mail me their toplogy file? If the parameters are

Re: [gmx-users] access code for qmmm

2009-11-17 Thread Farzad Molani
Hi Ilona, I saw the web adress. unfortunetly we don't have gaussian and gamess uk. I want to calculate QM region by ab inition or DFT methods. which quantum mechanic package do I use?  Farzad Molani, Ph.D Student, Department of Theoretical Chemistry and Biochemistry, K. N. Toosi University of Te

RE: [gmx-users] ull code with defined negative relative displacements

2009-11-17 Thread Berk Hess
Hi, I would also like to be sure that everything works as I have intended it. So I guess the following input should work: pull = umbrella pull_geometry= direction pull_dim = N N Y pull_start = no pull_ngroups = 1 pull_group

[gmx-users] Re: access code for qmmm (Farzad Molani)

2009-11-17 Thread Gerrit Groenhof
http://www.kntu.ac.ir -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20091117/ca3182ed/attachment-0001.html -- Message: 7 Date: Tue, 17 Nov 2009 09:37:28 + From: "Kukol, A

[gmx-users] Urea Topology

2009-11-17 Thread karan syal
Dear All, I am looking for urea topology* (smith et al) *for gromos 96 force field. I tried searching through user contributions in gromacs site but couldnt find it. Is it possible for anyone who has already used it to mail me their toplogy file? -- gmx-users mailing listgmx-users@gromacs.org

RE: [gmx-users] access code for qmmm

2009-11-17 Thread Kukol, Andreas
GROMACS can do QM/MM. Andreas --- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Farzad Molani Sent: 17 November 2009 08:57 To: Discussion list for GROMACS users Subject: Re: [gmx-users] access code for qmmm Hello, Have you ever done

Re: [gmx-users] access code for qmmm

2009-11-17 Thread Farzad Molani
Hello, Have you ever done QM/MM? please introduce a free and good package for academic user. Thanks in advance Farzad Molani, Ph.D Student, Department of Theoretical Chemistry and Biochemistry, K. N. Toosi University of Technology, Tehran, Iran. Tel.: 009821 2306 4280 Fax: 009821 2285 3650 Web: