[gmx-users] Justin-lipid tutorial...

Hi Gromacs friends, I completed the justin lipid tutorials upto the three steps ... While performing the tutorial of lipid written by justin , I get following query.. 1. As per the tutorials we added the DPPC chain topology *; Include DPPC chain topology #include dppc.itp * dppc.itp file

RE: [gmx-users] Help with free energy

Hi Milinda, There are different methods to do Free energy. I am using Thermodynamics Integration method; hence if you are interested to use TI I am willing to guide you, but I never use bar method. I did some parametrization so if you float your topology and mpd files I will give you some idea

[gmx-users] Justin-lipid tutorial..

Hi Gromacs Friends, I am doing the justin-lipid tutorial..Link to the tutorial is ... http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html I made the g96_53a6_lipid force field as per the instruction of tutorial.. I have some queris regarding to these new force

Re: [gmx-users] a question about ensemble

Interesting discussion indeed. I'm just thinking that there might be no fundamental difference to other thermostats. There's nothing in the way that causes the friction, but then again, there's no physical particle that causes the stochastic term in v-rescale, and the Nosé-Hover particle is not

Re: [gmx-users] a question about ensemble

On Sat, 2012-05-05 at 13:19 +0200, Patrick Fuchs wrote: Interesting discussion indeed. I'm just thinking that there might be no fundamental difference to other thermostats. There's nothing in the way that causes the friction, but then again, there's no physical particle that causes the

[gmx-users] Topology parameters

Dear gmx users, I need to define a new residue topology ( Formyl ) in CHARMM27 force field. I have the formyl parameters for GROMOS. I'd like to know if the residue parameters are the same in different force fields? Thanks, Shima -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] choose a force field

Please be sure to keep the discussion on the gmx-users list and not my personal inbox. On 5/5/12 12:27 AM, Shima Arasteh wrote: You are right. Corresponding to the articles related to my project, CHARMM27 is often applied. I don't have any idea about CHARMM36,because I don't know it at all.

Re: [gmx-users] Justin-lipid tutorial...

On 5/5/12 2:50 AM, rama david wrote: Hi Gromacs friends, I completed the justin lipid tutorials upto the three steps ... While performing the tutorial of lipid written by justin , I get following query.. 1. As per the tutorials we added the DPPC chain topology *; Include DPPC chain

Re: [gmx-users] Justin-lipid tutorial..

On 5/5/12 4:01 AM, rama david wrote: Hi Gromacs Friends, I am doing the justin-lipid tutorial..Link to the tutorial is ... http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html I made the g96_53a6_lipid force field as per the instruction of tutorial.. I have

Re: [gmx-users] Topology parameters

On 5/5/12 9:21 AM, Shima Arasteh wrote: Dear gmx users, I need to define a new residue topology ( Formyl ) in CHARMM27 force field. I have the formyl parameters for GROMOS. I'd like to know if the residue parameters are the same in different force fields? Almost certainly not. Each force

[gmx-users] How to build 1-4 pairs tables for -tablep in mdrun?

Hi, all, I'm still confused about how to set up 1-4 interaction tables for tabulated non-bonding potentials when using the -tablep option in mdrun. The specific question is: How must I specify the 1-4 interaction in those tables? How many columns and with what? My primary goal is to set all the

Re: [gmx-users] How to build 1-4 pairs tables for -tablep in mdrun?

On 5/5/12 9:39 AM, Marcelo Lopez wrote: Hi, all, I'm still confused about how to set up 1-4 interaction tables for tabulated non-bonding potentials when using the -tablep option in mdrun. The specific question is: How must I specify the 1-4 interaction in those tables? How many columns and

Re: [gmx-users] Topology parameters

Can I use CHARMM-GUI  to get the formyl parameters for CHARMM36 and CHARMM27? Cheers, Shima From: Justin A. Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, May 5,

Re: [gmx-users] Topology parameters

On 5/5/12 11:39 AM, Shima Arasteh wrote: Can I use CHARMM-GUI to get the formyl parameters for CHARMM36 and CHARMM27? Maybe, try it and see. Swiss-Param might also be an option. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar

[gmx-users] how to use the triplets index file generated by g_hbond

Hello all, I have used g_hbond with -hbn option to generate a .ndx file that has Acceptor - Donor - Hydrogen in each line of the last index group. But I wonder I could I use this index file to monitor each hydrogen bond specified by these triplets along the trajectory? Also, I understand that

[gmx-users] keep the nanotube cylindrical.

Dear gmx users I am simulation a system including carbon nanotube+water.I have done these things: 1. I copied oplsaa.ff folder in my working directory 2. I added following lines to atomname2type.n2t C    opls_995    0  12.011  2    C  0.142  C 0.142 C    opls_996    0  12.011  3    C 

Re: [gmx-users] how to use the triplets index file generated by g_hbond

On 5/5/12 1:22 PM, Yun Shi wrote: Hello all, I have used g_hbond with -hbn option to generate a .ndx file that has Acceptor - Donor - Hydrogen in each line of the last index group. But I wonder I could I use this index file to monitor each hydrogen bond specified by these triplets along the

Re: [gmx-users] keep the nanotube cylindrical.

On 5/5/12 1:27 PM, Za Pour wrote: Dear gmx users I am simulation a system including carbon nanotube+water.I have done these things: 1. I copied oplsaa.ff folder in my working directory 2. I added following lines to atomname2type.n2t C opls_995 0 12.011 2 C 0.142 C 0.142 C opls_996 0 12.011 3

Re: [gmx-users] a question about ensemble

On Sat, 5 May 2012, Dommert Florian wrote: On Sat, 2012-05-05 at 13:19 +0200, Patrick Fuchs wrote: Interesting discussion indeed. I'm just thinking that there might be no fundamental difference to other thermostats. There's nothing in the way that causes the friction, but then again, there's

[gmx-users] Determining which parallelization algorithm I used

Hi, I think that Gromacs has two parallelization algorithms as of version 4.5: domain decomposition (the default) and particle decomposition. For my research, I am using the particle decomposition algorithm. Thus, I include the -pd switch when calling mdrun. However, I am worried that in one

Re: [gmx-users] Determining which parallelization algorithm I used

On 5/5/12 5:10 PM, Andrew DeYoung wrote: Hi, I think that Gromacs has two parallelization algorithms as of version 4.5: domain decomposition (the default) and particle decomposition. For my research, I am using the particle decomposition algorithm. Thus, I include the -pd switch when

[gmx-users] Glutamate Chi1 Dihedral Not Symmetrical?

Dear Gromacs Users, I am trying to plot the Ryckaert-Bellemans energy for rotating the chi1 dihedral of glutamate in protein. I tried to change the ch1 dihedral from 0-360 degrees at increments of 1 degree and saved the pdbs. Then I used the pdb's to obtain the corresponding gro files and a

[gmx-users] Chelation of Calcium with Citrate

Hi All, I would like to find the stoichiometry for the chelation of a calcium ion (Ca 2+) with a citrate ion (citrate 3-), as well as the equilibrium constant or free energy of calcium-citrate complex formation. x*Ca2+ + y*citrate3- = z*calcium-citrate-complex (x, y, and z are the

Re: [gmx-users] Determining which parallelization algorithm I used

On 6/05/2012 7:10 AM, Andrew DeYoung wrote: Hi, I think that Gromacs has two parallelization algorithms as of version 4.5: domain decomposition (the default) and particle decomposition. For my research, I am using the particle decomposition algorithm. Thus, I include the -pd switch when

Re: [gmx-users] Glutamate Chi1 Dihedral Not Symmetrical?

On 6/05/2012 9:27 AM, Sai Kumar Ramadugu wrote: Dear Gromacs Users, I am trying to plot the Ryckaert-Bellemans energy for rotating the chi1 dihedral of glutamate in protein. I tried to change the ch1 dihedral from 0-360 degrees at increments of 1 degree and saved the pdbs. Then I used the

Re: [gmx-users] How to build 1-4 pairs tables for -tablep in mdrun?

On 5/05/2012 11:39 PM, Marcelo Lopez wrote: Hi, all, I'm still confused about how to set up 1-4 interaction tables for tabulated non-bonding potentials when using the -tablep option in mdrun. The specific question is: How must I specify the 1-4 interaction in those tables? How many columns and

[gmx-users] how to keep nanotube cylindrical

Dear Justin I appreciate for your reply.I used -maxwarn option because grompp gave me: WARNING 1 [file ffbonded.itp, line 2705]:   Overriding Bond parameters.   old: 0.151 292880 0.151 292880   new: C   C  1   0.1418   478900 I guess I am not using improper in the topology file.my cnt.top file

Re: [gmx-users] how to keep nanotube cylindrical

On 5/5/12 10:21 PM, Za Pour wrote: Dear Justin I appreciate for your reply.I used -maxwarn option because grompp gave me: WARNING 1 [file ffbonded.itp, line 2705]: Overriding Bond parameters. old: 0.151 292880 0.151 292880 new: C C 1 0.1418 478900 OK, that's reasonable. I guess I am not

[gmx-users] the radius of dry core

Dear GROMACS Specialists, I am working about micelles and have a question about the radius of dry core. May I ask you to answer me, Please? In one paper, I saw that the radius of dry core equals where the density profiles of water and the surfactant hydrocarbon tails cross and a fraction of