Re: [gmx-users] Shift functions

2012-02-11 Thread Elisabeth
On 10 February 2012 09:41, Mark Abraham wrote: > On 11/02/2012 1:19 AM, Elisabeth wrote: > > > Hello all, >> >> Does the shift function use group based truncation? >> >> >> See the discussion of charge groups in manual section 3.4.2. >> > > Thanks Mark. > > -1- First of all if I am right cha

[gmx-users] Re: improper dihedral angle in charmm and opls aa (Mark Abraham)

2012-02-11 Thread Tom
Copls_2350.500 5 > > Oopls_236 -0.500 5 > > [ bonds ] > > N H > > NCA > > CAHA > > CACB > > CA C > > CB HB1 > > CB HB2 > > CBCG > > CG OD1 > >

[gmx-users] Umbrella Sampling

2012-02-11 Thread Steven Neumann
Dear Gmx Users, I run a simulation of a protein and 10 ligands. They all stacked on the protein surface. I extracted the coordinates of the somplex and I am doing Umbrella Sampling - I am trying to pull one of the ligand from my protein. My questions: Would you suggest restarining positions of the

[gmx-users] Re: improper dihedral angle in charmm and opls aa (Mark Abraham)

2012-02-11 Thread Mark Abraham
HB1 > CB HB2 > CBCG > CG OD1 > CG ND2 >ND2 HD21 >ND2 HD22 > C O > -C N > [ dihedrals ] ; override some with residue-specific ones > NCA CB CG dih_ASN_chi1_N_C_

[gmx-users] co-solvent simulation

2012-02-11 Thread Yao Yao
I am simulating a protein in glycerol solution in amber03 ff and followed "http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents";. Since glycerol is not available in amber03.ff by default, I built it in the ffbonded.itp and aminoacids.rtp. For test purpose, I then made a itp for it and sol

[gmx-users] co-solvent simulation

2012-02-11 Thread Yao Yao
I am simulating a protein in glycerol solution in amber03 ff and followed "http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents";. Since glycerol is not available in amber03.ff by default, I built it in the ffbonded.itp and aminoacids.rtp. For test purpose, I then made a itp for it and

Re: [gmx-users] co-solvent simulation

2012-02-11 Thread Mark Abraham
On 12/02/2012 4:16 PM, Yao Yao wrote: I am simulating a protein in glycerol solution in amber03 ff and followed "http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents";. Since glycerol is not available in amber03.ff by default, I built it in the ffbonded.itp You should not need to touch

Re: [gmx-users] co-solvent simulation

2012-02-11 Thread Yao Yao
Hi Mark, Thanks for your reply. I have not figured out what the problem. BUt I am thinking if I have two proteins in my system, like simulating the protein-protein interaction, what I should call the second protein for [moleculetype] in my .top, still "protein"? Thanks, Yao __

[gmx-users] co-solvent simulation

2012-02-11 Thread Yao Yao
Actually even I follow the ""http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents"and try the built-in ureaas co-solvent, it has the same problem (solvate urea as protein can work, but does not work if you consider it as co-solvent). I do not know if anyone has met the same problem befo

Re: [gmx-users] co-solvent simulation

2012-02-11 Thread Yao Yao
Please disregard my previous email. I made a minor mistake when I built the .top file. Thanks, Yao From: Yao Yao To: "gmx-users@gromacs.org" Sent: Saturday, February 11, 2012 11:06 PM Subject: [gmx-users] co-solvent simulation Actually even I follow the