[gmx-users] pullf.xvg

Could someone please tell me what exactly is printed in the pullf.xvg file from an umbrella sampling simulation? Is it the total force acting the COM of the pull group - i.e. force from regular potential plus the umbrella force or just the unbiased force? Krzysztof Kuczera -- Krzysztof

Re: [gmx-users] REMD - low temperature ranges

sample the folded state. Another reason might be having experimental data at lower T, but this is problematic, as it is hard to model temperature-dependent properties with simple force fields. Krzysztof Kuczera On 4/27/12 10:06 AM, Tomek Wlodarski wrote: Hi Mark, Thanks for reply. The problem is

Re: [gmx-users] protein and DMPC in Charmm36 ff

atom names in the lipids Krzysztof Kuczera On 4/15/12 12:09 PM, Tomek Wlodarski wrote: Hi, I would like to simulate protein in DMPC bilayer in Charmm36 ff. I checked mailing list and KALP-15 tutorial, but still I have a few basic questions. 1) I have problem with DMPC bilayer... - VMD membrane

Re: [gmx-users] Velocity autocorrelation

You probably need to save velocities at least every 10 fs; look at your plot on a fine enough time scale - say 0-1 ps range probably running in NVE ensemble would help as well Krzysztof Kuczera On 3/29/12 10:42 AM, Ignacio Fernández Galván wrote: Dear all, I'm trying to estimat

[gmx-users] CHARMM27 topology for DOPC

( the 100 ns solvated bilayer simulation is already on my list) Greetings Krzysztof Kuczera -- Krzysztof Kuczera Departments of Chemistry and Molecular Biosciences The University of Kansas 2010 Malott Hall Lawrence, KS 66045 Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu http

Re: [gmx-users] ACE - NME caps

are found. It would be very helpful if I could find the parameters of ACE and NME caps for the charmm27 force field and the parameters of NME for gromos43a1 and gromos53a6, in order to integrate them in the parameter files of Gromacs. Thanks in advance -- Krzysztof Kuczera Professor

Re: [gmx-users] adding hydrogen

ones) ? Thanks, -- Krzysztof Kuczera Professor Departments of Chemistry and Molecular Biosciences The University of Kansas 2010 Malott Hall Lawrence, KS 66045 Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu http://oolung.chem.ku.edu/~kuczera/home.html -- gmx-users mailing listgmx-users@g

Re: [gmx-users] Cytochrom C

rsion of Gromacs. 4.5.4 and lower don't have ACE in charmm27. On 2012-01-06 12 :59:56PM -0600, Krzysztof Kuczera wrote: > Here is the blocking group from > gromacs-4.5.5/share/top/charmm27.ff/aminoacids.rtp > KK >

Re: [gmx-users] Cytochrom C

www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Krzysztof Kuczera Professor Departments of Chemistry and Molecular Biosciences The University of Kansas 2010 Malott Hall Lawrence, KS 66045 Tel: 785-864-5060 Fax: 785-864-539

Re: [gmx-users] barostat for gases

)? Thanks. -- Krzysztof Kuczera Departments of Chemistry and Molecular Biosciences The University of Kansas 2010 Malott Hall Lawrence, KS 66045 Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu http://oolung.chem.ku.edu/~kuczera/home.html -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] ACE patch for CHARMM27

wrote: Krzysztof Kuczera wrote: Hi GMXers, I am interested in simulating blocked peptides with CHARMM (and other force fields), using gromacs-4.5, and would appreciate some help from more experienced GROMACS users on details. To test things out I made a stab at creating an ACE N-terminal patch -

[gmx-users] ACE patch for CHARMM27

-- Krzysztof Kuczera Departments of Chemistry and Molecular Biosciences The University of Kansas 2010 Malott Hall Lawrence, KS 66045 Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu http://oolung.chem.ku.edu/~kuczera/home.html ala5_alpha.pdb Description: Protein Databank data -- gmx

Re: [gmx-users] Re: Help regading Gromacs

Prabha. K -- Krzysztof Kuczera Professor Departments of Chemistry and Molecular Biosciences The University of Kansas 2010 Malott Hall Lawrence, KS 66045 Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu http://oolung.chem.ku.edu/~kuczera/home.html -- gmx-users mailing list

Re: [gmx-users] Incorrect C-terminal in peptide starting with GLY

U ends up with incorrect charge and qtot is not an integer Without the '-inter', the system gets GLY-NH3+ and GLY-COO- as well ... Could someone suggest a fix for this ? Regards Krzysztof -- Krzysztof Kuczera Departments of Chemistry and Molecular Biosciences The Universit

[gmx-users] Incorrect C-terminal in peptide starting with GLY

ystem gets GLY-NH3+ and GLY-COO- as well ... Could someone suggest a fix for this ? Regards Krzysztof -- Krzysztof Kuczera Departments of Chemistry and Molecular Biosciences The University of Kansas 2010 Malott Hall Lawrence, KS 66045 Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@k

[gmx-users] "simulated long enough" message from tpbconv

r point - why is the total number of steps not a multiple of 10/0.002 = 5000, while the time remains in multiples of 10 ps ? Thanks for any ideas Krzysztof -- Krzysztof Kuczera Departments of Chemistry and Molecular Biosciences The University of Kansas 2010 Malott Hall Lawrence, KS