[gmx-users] Dihedral angle in OPLS-AA force field

Dear All, I have a basic question on Dihedral angle in OPLS-AA force field. I read some of the papers related to development of OPLS force field where they have different formula for calculating the torsion angle I think that is Ryckaert-Bellemans function, but there is no separate term for Impro

Re: [gmx-users] Gromacs version

Hi Raghu, First of all, if all conditions are equal the two simulations should be drawn from the same ensemble and should for that reason be "comparable". However, some routines have changed and we don't really know whether and how this might influence the ensemble. The best way to check is to co

[gmx-users] constraint distance

Dear All    I would like to know how to constraint the distance between the different molecule, ex. the ligand and the protein. As far as I know whatever to do the constraint, distance, angle dihedral, it can do just in the same molecule.     Thank you in advance for all of your help.With B

Re: [gmx-users] May I use "-b" and "- e" in the cosine con tent calculation of PC?

Hi Mao-Cai Yan, A high cosine content usually means you're not in equilibrium, or your trajectory includes the part in which the system is going to equilibrium. Now, apparently, you're not interested in equilibrium, but rather in some event of change, which may be required to go from the starting

Re: [gmx-users] constraint distance

Hi Kanin, The only way to get away with that is to merge your two parts to form one molecule, with the only connection being a distance_restraint (or another bonded term if you want to emulate bond-like behaviour such as a salt-bridge). Best, Tsjerk On 9/11/06, kanin wichapong <[EMAIL PROTECTE

[gmx-users] Re: problem with dimer simulation !

try - cluster, and then as cluster group protein.Kay. hello, Kay   thanks so much for your advice, but with -pbc cluster, one of the two peptides still move out of the box and frequently jump back. i have no idea about it, any else should i do ?   best regards,   Liang   _

[gmx-users] Re: problem with dimer simulation !

hi cw,using trjconv -pbc nojump should remove the jumps. then you can analyse interactions between different chains, while it doesn't matter for the analysis where they diffuse.daniela hello, daniela   thanks for your reply, it really doesn't matter when i calculate the distance between two

[gmx-users] May I use "-b" and "- e" in the cosine co n tent calculation of PC?

Thank you, Tsjerk & David. Judging from RMSD and other analysis, the system has been in well equilibrium at 5 ns; (however, the cosine contents of last 25 ns and whole 30 ns are also higher than 0.7.) The RMSD during the last 25 nanoseconds (compared to the conformation at 5ns) is within 0.25 nm. A

Re: [gmx-users] constrained minimization

이 선주 wrote: Dear All I just saw from the mailing list that David answered that the restrained minimization can be done and it is different from the constrained minimization. For the torsional parameter optimization, I think I need to run minimization after constraining torsion angles. Does an

[gmx-users] genion causing atom to be in multiple T-Coupling groups

Dear Users, I'm hoping for an answear on my problem with neutralizing my system adding 3 Cl ions with genion. When running grompp after genion with the new generated .gro file I get this error: Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1) which is the last water atom (tot

Re: [gmx-users] genion causing atom to be in multiple T-Coupling groups

Una Bjarnadottir wrote: Dear Users, I'm hoping for an answear on my problem with neutralizing my system adding 3 Cl ions with genion. When running grompp after genion with the new generated .gro file I get this error: Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1) which i

SV: Re: [gmx-users] constraint distance

 Hi,  maybe I am misunderstanding either the manual or the topic.. but - in my world -  I never stop being puzzled by the part of chapt 6 in the manual which apparently  says that such distance constraining is possible even though it (seems) to be  secretly known that it is _not_ possible unless on

Re: SV: Re: [gmx-users] constraint distance

Soren Enemark wrote: Hi, maybe I am misunderstanding either the manual or the topic.. but - in my world - I never stop being puzzled by the part of chapt 6 in the manual which apparently says that such distance constraining is possible even though it (seems) to be secretly known that it i

Re: [gmx-users] Re: problem with dimer simulation !

C.W. Liang wrote: try - cluster, and then as cluster group protein. Kay. hello, Kay thanks so much for your advice, but with -pbc cluster, one of the two peptides still move out of the box and frequently jump back. i have no idea about it, any else should i do ? merge the peptides into on

Re: SV: Re: [gmx-users] constraint distance

> Hi, > maybe I am misunderstanding either the manual or the topic.. but - in my > world - > I never stop being puzzled by the part of chapt 6 in the manual which > apparently > says that such distance constraining is possible even though it (seems) > to be > secretly known that it is _not

Re: [gmx-users] Dihedral angle in OPLS-AA force field

[EMAIL PROTECTED] wrote: Dear All, I have a basic question on Dihedral angle in OPLS-AA force field. I read some of the papers related to development of OPLS force field where they have different formula for calculating the torsion angle I think that is Ryckaert-Bellemans function, but there is

Re: [gmx-users] genion causing atom to be in multiple T-Coupling groups

> Dear Users, > > I'm hoping for an answear on my problem with neutralizing my system adding > 3 Cl ions with genion. When > running grompp after genion with the new generated .gro file I get this error: > > Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1) Read closely - "T-Coupli

Re: [gmx-users] Dihedral angle in OPLS-AA force field

[EMAIL PROTECTED] wrote: Dear All, I have a basic question on Dihedral angle in OPLS-AA force field. I read some of the papers related to development of OPLS force field where they have different formula for calculating the torsion angle I think that is Ryckaert-Bellemans function, but there is

SV: Re: SV: Re: [gmx-users] constraint distance

David van der Spoel <[EMAIL PROTECTED]> skrev: Soren Enemark wrote:> Hi,> maybe I am misunderstanding either the manual or the topic.. but - in > my world -> I never stop being puzzled by the part of chapt 6 in the manual which > apparently> says that such distance constraining is possible even

[gmx-users] Re: genion causing atom to be in multiple T-Coupling groups

Una Bjarnadottir wrote: Dear Users, I'm hoping for an answear on my problem with neutralizing my system adding 3 Cl ions with genion. When running grompp after genion with the new generated .gro file I get this error: Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1) which

[gmx-users] RE: gmx-users Digest, Vol 29, Issue 23

Title: RE: gmx-users Digest, Vol 29, Issue 23 Message: 6 Date: Sun, 10 Sep 2006 18:02:50 -0700 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] TFE .gro files To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-88

Re: [gmx-users] Re: genion causing atom to be in multiple T-Coupling groups

Una Bjarnadottir wrote: Una Bjarnadottir wrote: Dear Users, I'm hoping for an answear on my problem with neutralizing my system adding 3 Cl ions with genion. When running grompp after genion with the new generated .gro file I get this error: Fatal error: Atom 33000 in multiple T-Coupling

Re: [gmx-users] RE: gmx-users Digest, Vol 29, Issue 23

Copps, Jeffrey wrote: Message: 6 Date: Sun, 10 Sep 2006 18:02:50 -0700 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] TFE .gro files To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Copps,

[gmx-users] Free energy, frozen atoms and exclusions

Hi all, I'm trying to calculate solvation free energies and I've found something "strange". The thing is I'm interested in free energy of rigid molecules (I consider other contributions separately), typically a small solute molecule in water. I'm making a test with methanol. The setup is a frozen

RE: [gmx-users] Free energy, frozen atoms and exclusions

From: Ignacio Fernández Galván <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] Free energy, frozen atoms and exclusions Date: Mon, 11 Sep 2006 15:18:01 +0100 (BST) Hi all, I'm trying to calculate solvation free energies and I've

RE: [gmx-users] Free energy, frozen atoms and exclusions

--- Berk Hess <[EMAIL PROTECTED]> wrote: > >Is there something I'm missing? A bug/feature in the code? A > >limitation? > > If you are using PME, the mesh contribution is not excluded when > using energygrp_excl, grompp should give you a warning about this. > Adding all the pairs as exclusions so

[gmx-users] constraint distance between ligand and protein

Hi All,    I would like to know how to make a distance constraint between the ligand and the protein. If I just merge two chain together by pdb2gmx, it can done if the two chain are both protein. However, if it is a ligand and protein, i can't merge together because there is no libraly for the liga

[gmx-users] File input/output error: Can not determine precision of trn file

Hello everyone, It seems that one of my trajectory files has an error. I get the following message when using trjconv -f trajectory.trr. File input/output error: Can not determine precision of trn file I noticed that there was a previous question about this error message. However, the only availa

[gmx-users] Re: constrained minimization (David van der Spoel)

> Dear All > > I just saw from the mailing list that David answered that the restrained > minimization can be done and it is different from the constrained > minimization. For the torsional parameter optimization, I think I need > to run minimization after constraining torsion angles. Does anyo

[gmx-users] OPLS-AA force field again regarding 1-4 interaction

Thanks David for your reply, I have a another doubt on OPLS force field regarding 1-4 interaction. In manual (chapter 4 page no 62) it was written The use of RB potential implies exclusion of LJ interaction between first and the last atom of the dihedral (mean 1-4 interaction).So why I am getting

[gmx-users] Re: Gromacs-CPMD: QMMM

Hi Amit, Please open epot.inc in SOURCE folder of CPMD-3.11.1, search for MAXNEAR and change the statement: PARAMETER (MAXNEAR=2000) to PARAMETER (MAXNEAR=5000) best, pb. On Sep 11, 2006, at 3:52 PM, [EMAIL PROTECTED] wrote: Dear Dr. Biswas, I am getting following error while running groma

[gmx-users] unsubscribe

[EMAIL PROTECTED] -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: sexta-feira, 8 de Setembro de 2006 2:46 To: gmx-users@gromacs.org Subject: [gmx-users] Re: Simulation problem with extended membrane system! Having actually looked

[gmx-users] Re: Simulation problem with extended membrane system!

I just remembered that I previously posted a script to assist in removing waters based on their z position: http://www.gromacs.org/pipermail/gmx-users/2006-May/021526.html >Back to the previous question, after solvate the lipids in water, can I >remove the water placed in the membrane with excel

[gmx-users] problem about "order parameter"

I am performing some simulation about common protein.I am puzzled when I want to get the order parameter(S2, N-H bond in main chian) to compare with the result of my NMR experiment.Who can give me a detailed way to get this parameter in Gromacs3.3.1? Thanks ! ==

Re: [gmx-users] problem about "order parameter"

clark wrote: I am performing some simulation about common protein.I am puzzled when I want to get the order parameter(S2, N-H bond in main chian) to compare with the result of my NMR experiment. Who can give me a detailed way to get this parameter in Gromacs3.3.1? Thanks ! g_rotacf you n

[gmx-users] changing the parameter numbers for torsion

hello,gmx-users i have a force field that contain 7 rychaert-bellemans dihedral coefficients, but in gromacs there are only 6, how can i manage it ? and where i should change the source code? regards! thanks! Rongliang Wu [EMAIL PROTECTE

Re: [gmx-users] changing the parameter numbers for torsion

Rongliang Wu wrote: hello,gmx-users i have a force field that contain 7 rychaert-bellemans dihedral coefficients, but in gromacs there are only 6, how can i manage it ? and where i should change the source code? maybe you can combine a RB with a proper dihedral with n=7 over th

[gmx-users] re: non-bonded interactions in GROMACS

>In manual (chapter 4 page no 62) it was written The use of RB potential >implies exclusion of LJ interaction between first and the last atom of the >dihedral (mean 1-4 interaction).So why I am getting LJ-14 and Coulomb-14 >energy in my log file (see below) is there is any problem in this >sim