[gmx-users] MD run for octanol system

Hi There, I am trying to run MD simulation for octanol using GROMACS, I have downloaded the octanol.tar.gz from the user contributed section http://www.gromacs.org/@api/deki/files/18/=octanol.tar.gz. When I performed this MD run according to the run input file and molecule topology provided in

[gmx-users] ffamber99sb error

Dear GROMACS users, I'll be most thankful for any comment/help you might have regarding the following error that I'm encountering in grompp_d : Atomtype amber99_34 not found In ffamber99sb.rtp, amber99_34 refers to the N atom of each amino acid. Thanks a lot Arik -- gmx-users mailing list

Re: [gmx-users] Re: g_cluster settings

Marc - Note that you used the linkage method which maps a structure to a cluster if its distance to any structure already in the cluster is is less than the cutoff. If you think it's not representative of your system try another clustering method, but note that you may need a longer trajectory as

Re: [gmx-users] MD run for octanol system

Hi, try converting (trjconv) your trajectory using the flag -pbc res or -pbc mol Esteban -- On Mon, Jul 12, 2010 at 8:45 AM, vivek sharma viveksharma.i...@gmail.comwrote: Hi There, I am trying to run MD simulation for octanol using GROMACS, I have downloaded the octanol.tar.gz from the user

[gmx-users] Where can I dowload DSSP program?

Hi GMX users,    I am interested in doing dssp analysis. Where can I download dssp program? I apprecitate if you could send the web address for it.  with thanks ***+ Dr.Karunakaran Chandran+ Biophysics Department + Medical College of Wisconsin

Re: [gmx-users] Where can I dowload DSSP program?

Hello This link will help - http://swift.cmbi.ru.nl/gv/dssp Regards Ajeeta On Mon, Jul 12, 2010 at 3:41 PM, chandran karunakaran ckaru2...@yahoo.comwrote: Hi GMX users, I am interested in doing dssp analysis. Where can I download dssp program? I apprecitate if you could send the web

[gmx-users] Re: MD run for octanol system

Hmm... Straight lines... Is it VMD that your used to visualize the trajectory? I think this is just due to PBC. Compute some RDFs and they will give you an answer if your system is healthy. Dr. Vitaly Chaban I am trying to run MD simulation for octanol using GROMACS, I have downloaded the

[gmx-users] Re: ffamber99sb error

Arik: Your topology file(s) are welcome in order to provide help. Vitaly I'll be most thankful for any comment/help you might have regarding the following error that I'm encountering in grompp_d : Atomtype amber99_34 not found In ffamber99sb.rtp, amber99_34 refers to the N atom of each

[gmx-users] -tu flag in g_hbond

Hi gromacs users in g_hbond command there is not -tu flag and I want to have time unit as ns no default form (ps). What is the best way to do this? Please suggest. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] -tu flag in g_hbond

shahab shariati wrote: Hi gromacs users in g_hbond command there is not -tu flag and I want to have time unit as ns no default form (ps). What is the best way to do this? Please suggest. Either modify the code or simply change the axis labels in xmgrace. -Justin --

[gmx-users] -tu flag in g_hbond

Dear Justin thanks for your attention. this file that I want to be as ns is hbmap.xpm I did following steps to obtain pdf file : 1) xpm2ps 2) ps2pdf can I open xpm file by xmgrace? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] -tu flag in g_hbond

shahab shariati wrote: Dear Justin thanks for your attention. this file that I want to be as ns is hbmap.xpm I did following steps to obtain pdf file : 1) xpm2ps 2) ps2pdf can I open xpm file by xmgrace? No, you'll have to edit it by hand in a text editor. I was assuming you

[gmx-users] Re: selenium parameter

Susan. Please use the mailing list instead of personal email. A google search for electronegativity of selenium provides a useful first hit. The .rtp issue is covered often on the mailing list. Overall, you will find this link helpful:

[gmx-users] -tu flag in g_hbond

Dear Justin I opened my hbmap.xpm file by a text editor. first of file is as follows : /* XPM */ /* Generated by g_hbond */ /* This file can be converted to EPS by the GROMACS program xpm2ps */ /* title: Hydrogen Bond Existence Map */ /* legend: Hydrogen Bonds */ /* x-label: Time (ns) */ /*

[gmx-users] -tu flag in g_hbond

Dear Justin *excuseme this email is true.* I opened my hbmap.xpm file by a text editor. first of file is as follows : /* XPM */ /* Generated by g_hbond */ /* This file can be converted to EPS by the GROMACS program xpm2ps */ /* title: Hydrogen Bond Existence Map */ /* legend: Hydrogen Bonds

Re: [gmx-users] number of degrees of frredom

Moeed wrote: Dear Justin, The actual box I got by replicating monomer units has size of 15 0.5 0.5 That is chain has no space to move. I know you have already given me some tips on high repulsion in the system but that had to do with incorrect topology file. I assure you I have learned

[gmx-users] Re: number of degrees of frredom

the LINCS constraint for all bonds constraint-algorithm = lincs -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100712/21962bb6/attachment.html -- -- gmx-users mailing

[gmx-users] OPLS-2005 forcefield parameters for carbohydrates in Gromacs 4.0.7?

Hello, I'm using Gromacs 4.0.7, and I'm looking for the OPLS-2005 all-atom forcefield, which I'm told contains parameters and residue topologies that will allow me to model beta (1-4) cellobiose. Does the standard OPLS-AA parameter set supplied with Gromacs 4.0.7 contain the OPLS-2005 parameters

[gmx-users] question about dynamics

Hi, all: I am studying thermal expansion of bulk crystal solid. I want to reach the state with 300K in temperature and 1 bar pressure. I am not sure whether my procedure is correct or not. First I run energy minimization, then a constant volume for temperature coupling ( integrator is

Re: [gmx-users] question about dynamics

Shuangxing Dai wrote: Hi, all: I am studying thermal expansion of bulk crystal solid. I want to reach the state with 300K in temperature and 1 bar pressure. I am not sure whether my procedure is correct or not. First I run energy minimization, then a constant volume for temperature

[gmx-users] dissolution of gases in liquid

Hi all, We are trying to calculate the solubility of argon in water using the partial densities function. The following traditional MD setup is used. The water (=4000) is in the center of the box and is surrounded by the argon atoms (=50) along Z direction. The electrostatics is treated with PME,

Re: [gmx-users] amber/charmm force field and HB lifetime at low temperature

Hi Mark, Thanks for your reply. I used charmm forcefield to study a solvated protein using TIP5P water model applying NVT ensemble. I did hydrogen-bond correlation function to understand the diffusivity of water near the protein. At 300K the result came out fine and comparable with the

[gmx-users] Fwd: dissolution of gases in liquid

In addition, we also tried to equilibrate the liquid-gas interface in the NVT and then switched on barostat. The result with barostat was unfortunately the same. I suspect the problem is in the (anisotropic) pressure coupling but I still have no idea how it can be corrected. The described setup is

[gmx-users] g_msd

Dear gromacs users I make a MD of 20 ns of a solute in water With the g_msd program the msd vs the time was obtained In the plot, I observed a linear behaviour of the MSD from 0 to 15 ns and a plateau with no linear tendence at the last 5 ns arpoximately. In order to know if the observed

Re: [gmx-users] question about dynamics

Thanks for the help. The error information is: Using Berendsen pressure coupling invalidates the true ensemble for the thermostat. Do you have any idea of this information? Thanks, Shuangxing Dai On Jul 12, 2010, at 15:43, Justin A. Lemkul jalem...@vt.edu wrote: Shuangxing Dai wrote:

Re: [gmx-users] question about dynamics

Shuangxing Dai wrote: Thanks for the help. The error information is: Using Berendsen pressure coupling invalidates the true ensemble for the thermostat. Do you have any idea of this information? The Berendsen method does not produce a proper ensemble for either temperature or pressure.

[gmx-users] Compile-time errors with MKL

Hello there! I'm trying to compile gromacs 4.0.7 with icc, mkl and openmpi. The problem is that, when I set the environment to LDFLAGS=-L/home/opt/intel/cmkl/10.2.5.035/lib/em64t/ -L/usr/lib CPPFLAGS=-I/home/opt/intel/cmkl/10.2.5.035/include/ and edit line 26576 of ./config to read

Re: [gmx-users] g_msd

On Mon, Jul 12, 2010 at 5:22 PM, Ricardo Cuya Guizado rcu...@hotmail.com wrote: Dear gromacs users I make a MD of 20 ns of a solute in water With the g_msd program the msd vs the time was obtained In the plot, I observed a linear behaviour of the MSD from 0 to 15 ns and a plateau with no

Re: [gmx-users] g_msd

On 13/07/10 07:22, Ricardo Cuya Guizado wrote: Dear gromacs users I make a MD of 20 ns of a solute in water With the g_msd program the msd vs the time was obtained In the plot, I observed a linear behaviour of the MSD from 0 to 15 ns and a plateau with no linear tendence at the last 5 ns

Re: [gmx-users] Compile-time errors with MKL

On 13/07/10 08:20, Elton Carvalho wrote: Hello there! I'm trying to compile gromacs 4.0.7 with icc, mkl and openmpi. The problem is that, when I set the environment to LDFLAGS=-L/home/opt/intel/cmkl/10.2.5.035/lib/em64t/ -L/usr/lib CPPFLAGS=-I/home/opt/intel/cmkl/10.2.5.035/include/ and

[gmx-users] grommp_md error

Hello, Sorry I did not paste the error message part properly. Initially I am trying to study PE in vacuum (current box size 30*30*30 nm) and then I will solvate the PE with Hexane. NOTE 1 [file md-July11-NPTcompression.mdp, line unknown]: The Berendsen thermostat does not generate the correct

Re: [gmx-users] grommp_md error

Moeed wrote: Hello, Sorry I did not paste the error message part properly. Initially I am trying to study PE in vacuum (current box size 30*30*30 nm) and then I will solvate the PE with Hexane. NOTE 1 [file md-July11-NPTcompression.mdp, line unknown]: The Berendsen thermostat does not

[gmx-users] Re: grommp_md error

Moeed: I think you make the things more complicated than they really are. 2- I have a question about doing NPT for compressing the system. Can I also do NVT for a short time and when the chain has a more realistic structure , take that structure and change the volume myself? I am just asking

[gmx-users] Stabilizing a heavy metal ion in solution

Dear users, I would like to know if users can give me a couple of suggestions on how to control large temperature swings of a heavy metal ion like Uranium in solution. The temperature of the metal ion fluctuates considerably and hardly stabilizes--even in the long time limit while the solvent