[gmx-users] how to find conformational free energy?

can anyone tell me how to find the conformational free energy? i have the one peptide which have 12 amino residue. i was run the simulation. and found the g_energy from trajectory file. i have potential energy. now i want to find the conformational free energy and entropy and enthalpy. any one kno

Re: [gmx-users] how to find conformational free energy?

ajani haresh wrote: can anyone tell me how to find the conformational free energy? i have the one peptide which have 12 amino residue. i was run the simulation. and found the g_energy from trajectory file. i have potential energy. now i want to find the conformational free energy and entropy and

Re: [gmx-users] grompp error in running simultion of membrane protein with lipid bilayer

nitu sharma wrote: Dear all, I am trying to do simulation of membrane protein with lipid bilayer for this I have made topology file like this- ; topology for tap in 128 dmpc lipids plus water. ; rr1_A.itp and rr1_B.itp can be made in a straightforward manner with pdb2gmx

[gmx-users] Re: PDB structure quality

We've recently announced iCing, which includes whatif as well. Please, take a look at http://nmr.cmbi.ru.nl/cing/Home.html. If it happens that your complex is from NMR and deposit in PDB so you can find it here (http://nmr.cmbi.ru.nl/NRG-CING/index/index.html) already evaluated. Cheers, Alan On F

[gmx-users] New topology generation tool available

Hi All, I have added a new program to the Users' Contributions section of the website. TopolGen is yet another topology-building tool that will produce a rough OPLS-AA-compatible topology from an all-atom PDB file. Please refer to the README included with the program (written in Perl) for sp

[gmx-users] query regarding coming out of ligand from protein during simulation

Dear all,           I am trying to perform simulation of a protein with several ligands, in case of certain ligands I found that the ligand  is coming out of the protein after 5-6 ns. I have checked the energy of the system, but it does not show any abrupt change, still the ligand is coming out

Re: [gmx-users] query regarding coming out of ligand from protein during simulation

sangeeta kundu wrote: Dear all, I am trying to perform simulation of a protein with several ligands, in case of certain ligands I found that the ligand is coming out of the protein after 5-6 ns. I have checked the energy of the system, but it does not show any abrupt change, s

[gmx-users] Hydrogen bonds from interface - gOH(z)

Hi everyone, I am working with water in interface with air and I would examine how the hydrogen bonds vary with the distance from the interface. Something like that ( http://pubs.acs.org/appl/literatum/publisher/achs/journals/production/langd5/2009/langd5.2009.25.issue-3/la803324x/images/large/la-2

[gmx-users] How to find Enthalpy And Entropy ?

Hello, I have trajectory file. i was run simulation at 20ns. they genrate the trajectory file. i was also found the g_energy and g_rmsd. i want to find the Enthalpy and Entropy of this peptide simulation. so i can know abt these peptide conformation. any one know how to find the enthalpy and ent

[gmx-users] Couette flow

Hi, With reference to http://www.mail-archive.com/gmx-users@gromacs.org/msg13374.html I would like to know if anybody has successfully simulated couette flow using GROMACS. If yes, then please suggest what specific steps has to be taken. If no, then are the developers planning to implement givin

Re: [gmx-users] How to find Enthalpy And Entropy ?

ajani haresh wrote: Hello, I have trajectory file. i was run simulation at 20ns. they genrate the trajectory file. i was also found the g_energy and g_rmsd. i want to find the Enthalpy and Entropy of this peptide simulation. so i can know abt these peptide conformation. any one know how

Re: [gmx-users] Couette flow

Manik Mayur wrote: Hi, With reference to http://www.mail-archive.com/gmx-users@gromacs.org/msg13374.html I would like to know if anybody has successfully simulated couette flow using GROMACS. If yes, then please suggest what specific steps has to be taken. If no, then are the developers plan

Re: [gmx-users] Couette flow

On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel wrote: > Manik Mayur wrote: > >> Hi, >> >> With reference to >> >> http://www.mail-archive.com/gmx-users@gromacs.org/msg13374.html >> >> I would like to know if anybody has successfully simulated couette flow >> using GROMACS. If yes, then please

Re: [gmx-users] Couette flow

Manik Mayur wrote: On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel mailto:sp...@xray.bmc.uu.se>> wrote: Manik Mayur wrote: Hi, With reference to http://www.mail-archive.com/gmx-users@gromacs.org/msg13374.html I would like to know if anybody has suc

Re: [gmx-users] Couette flow

On Fri, Apr 3, 2009 at 9:48 PM, David van der Spoel wrote: > Manik Mayur wrote: > >> >> >> On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel >> > sp...@xray.bmc.uu.se>> wrote: >> >>Manik Mayur wrote: >> >>Hi, >> >>With reference to >> >>http://www.mail-archive.com/gm

Re: [gmx-users] Couette flow

Manik Mayur wrote: On Fri, Apr 3, 2009 at 9:48 PM, David van der Spoel mailto:sp...@xray.bmc.uu.se>> wrote: Manik Mayur wrote: On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel mailto:sp...@xray.bmc.uu.se>

Re: [gmx-users] Couette flow

On Fri, Apr 3, 2009 at 10:47 PM, David van der Spoel wrote: > Manik Mayur wrote: > >> >> >> On Fri, Apr 3, 2009 at 9:48 PM, David van der Spoel >> > sp...@xray.bmc.uu.se>> wrote: >> >>Manik Mayur wrote: >> >> >> >>On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel >>mailto:sp

Re: [gmx-users] Couette flow

Manik Mayur wrote: On Fri, Apr 3, 2009 at 10:47 PM, David van der Spoel mailto:sp...@xray.bmc.uu.se>> wrote: Manik Mayur wrote: On Fri, Apr 3, 2009 at 9:48 PM, David van der Spoel mailto:sp...@xray.bmc.uu.se>

[gmx-users] dssp install problems

All, I've looked at the site and cannot figure this out, so apologies if this is a painful often seen question. I'm trying to install dssp for use with do_dssp on an OSX.5 PPC system with the following steps, in the dssp folder: ./DsspCompileCC cd.. sudo mv dssp /usr/local cd /usr/loca

Re: [gmx-users] Couette flow

On Fri, Apr 3, 2009 at 11:11 PM, David van der Spoel wrote: > Manik Mayur wrote: > >> >> >> On Fri, Apr 3, 2009 at 10:47 PM, David van der Spoel < >> sp...@xray.bmc.uu.se > wrote: >> >>Manik Mayur wrote: >> >> >> >>On Fri, Apr 3, 2009 at 9:48 PM, David van

Re: [gmx-users] dssp install problems

KS Rotondi wrote: All, I've looked at the site and cannot figure this out, so apologies if this is a painful often seen question. I'm trying to install dssp for use with do_dssp on an OSX.5 PPC system with the following steps, in the dssp folder: ./DsspCompileCC cd.. sudo mv dssp /usr/

Re: [gmx-users] dssp install problems

Hi, Try this: cd /usr/local/bin sudo ln -s dsspcmbi dssp Hope this help, Rui Rodrigues On Fri, 3 Apr 2009 13:44:56 -0400, KS Rotondi wrote > All, > > I've looked at the site and cannot figure this out, so apologies if > this is a painful often seen question. > > I'm trying to install dssp

Re: [gmx-users] dssp install problems

Many thanks to Mr. Lemkul and Mr. Rodrigues, their solution was, as they say, the ticket. Ken On Apr 3, 2009, at 1:57 PM, Justin A. Lemkul wrote: KS Rotondi wrote: All, I've looked at the site and cannot figure this out, so apologies if this is a painful often seen question. I'm trying t

[gmx-users] The free energy calculation in Manual Chapter 4

Hi I read the free energy calculation in Manual Chapter 4. What condition could I use this free energy calculation of the Gromacs MD package? >From tutorial, the solvation free energy can be calculated by Gromacs. how about the free energy of the micelle forming system? Can i apply the free energ

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRGassigned ones

I was thinking that's not such a problem switching tha OPLS-AA, since most of the atoms in my system are from water, that will remain being spc. -- From: "Lucio Ricardo Montero Valenzuela" Sent: Wednesday, April 01, 2009 12:59 AM To: "Discussion li

[gmx-users] Help on Exclusions and 1-4 Interactions

Dear all,   Recently,We have tried to implement our own version of frce felds into Gromacs 3.3.3. On the purpose of testing, we dumped out all the infrmation from tpr by using gmxdump. Everything goes fine except this 1-4 interactions terms. The prblem we had is that even though we had set numb

Re: [gmx-users] Help on Exclusions and 1-4 Interactions

feng chen wrote: Dear all, Recently,We have tried to implement our own version of frce felds into Gromacs 3.3.3. On the purpose of testing, we dumped out all the infrmation from tpr by using gmxdump. Everything goes fine except this 1-4 interactions terms. The prblem we had is that even th

[gmx-users] problem in topology file for protein+lipid bilayer system

Hello justin thanks for ur suggestion . I am trying to do membrane protein simulation with lipid bilayer . I have pdb file of inserted protein in dmpc lipid bilayer. But I am facing problem in making topology file for this system.As u told in previous mail you can't combine OPLS_AA with a standerd