Re: [gmx-users] GPU + surface

Hello. ¿Have you removed periodicity?. Because you may only be seeing traversal of water molecules among copies of the periodic system. Lucio Montero Ph. D. student Instituto de Biotecnologia, UNAM Mexico El 08/08/13 07:39, Ondrej Kroutil escribió: Dear GMX users. I have done simulation of

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

How can you calculate computationally charges for molecules containing phosphates? -- From: "Ran Friedman, Biochemisches Inst." Sent: Friday, March 27, 2009 2:35 PM To: ; "Discussion list for GROMACS users" Subject: Re: [gmx-users] HF/6-31G** E

Re: [gmx-users] simulation of protein in presence of ATP

Independently of your ATP position, your system may explode or show LINCS warnings if you use pressure and temperature coupling. I had these problem, and corrected it removing the pressure coupling. Pressure coupling will let your system expand in response to the heat, and if the positions are

Re: [gmx-users] Atomtype CMET not found

¿Did you change also the name of the “residue” (from 1MeOH to 1CH3OH (that is the “residue” name appearing in the RTP file))? Best regards Lucio From: Mina Madah Sent: Tuesday, November 16, 2010 6:00 AM To: gmx-users@gromacs.org Subject: [gmx-users] Atomtype CMET not found Dear all

Re: [gmx-users] Re:Question regarding Gromacs

If you are doing simulated annealing, your system explode if you are heating all the system (protein and water). Divide your system in protein and water and heat only the protein. -- From: "Tsjerk Wassenaar" <[EMAIL PROTECTED]> Sent: Monday, Septe

Re: [gmx-users] Integration of a carbonate ion to GROMACS V3.3

If you are using the GROMOS96, the forcefield files are ffG.*. ffgmx are for the GROMACS forcefield (that is deprecated). The forcefield file titles are listed in the file FF.dat in the gromacs topology directory. Here are the contents of my FF.dat file: 11 ffG43a1 GROMOS96 43a1 force fiel

[gmx-users] Force field selection

Hello! What is the best force field to use for a MD of a compley of three proteins and an organic molecule. And what are the best temperature and pressure coupling methods. Best regards. Lucio.___ gmx-users mailing listgmx-users@gromacs.org ht

Re: [gmx-users] How to show the created box?

If your box is very big, VMD may run out all your computer's memory and crash. You can copy your GRO file and erase some water molecules in the middle of the GRO file copy, for you see the extremes of your water box. Kind regards. -- From: "Mark A

Re: [gmx-users] OPLS-AA topologies for ATP/ADP.

Thanks very much. Lucio Montero. -- From: "Justin A. Lemkul" Sent: Wednesday, February 25, 2009 5:55 AM To: "Discusson list for GROMACS users" Subject: Re: [gmx-users] OPLS-AA topologies for ATP/ADP. Lucio Ricard

Re: [gmx-users] simulation box

If you use periodic boundaries, the box size needs to be more than twice the cutoffs, to avoid calculation errors. I found this advice in the manual. (I though reading it was a time waste, but more time I was going to waste doing a wrong 1 ns simulation on a big system). --

[gmx-users] Triclinic water box for a protein MD

aa (protein 1: 376 aa, protein 2: 132 aa, protein 3: 20 aa, complex size 64x64x104 Angstroms) surrounded by 12 Ângstroms of water. I want to run the MD simulating 20 ns. Best regards, Lucio Montero

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

How about MOPAC to calculate the charges for 3-methyladenine (this molecule has a charge +1) for using the G43a1 force field?. -- From: "Ran Friedman, Biochemisches Inst." Sent: Friday, March 27, 2009 2:35 PM To: ; "Discussion list for GROMACS us

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

How can you test the "ligands" when you don't know if they REALLY bind to the protein? -- From: "Ran Friedman, Biochemisches Inst." Sent: Friday, March 27, 2009 2:35 PM To: ; "Discussion list for GROMACS users" Subject: Re: [gmx-users] HF/6-31G

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

l-atom. Jorgensen himself uses OPLS-AA with TIP4P, so this is probably the best recommendation. Most important, if you chose to use another combination, you basically have to prove that this "works" as well (whatever that means...) > Mensaje citado por "Justin A. Lemkul" : >

Re: [gmx-users] Pressure Coupling Problem

I don't know the conditions you use with your system, but sometimes there are problems when you use pressure coupling in a system with positionally restrained or fixed atoms. Cheers. Lucio. From: Joe Joe Sent: Friday, April 10, 2009 12:12 PM To: Discussion list for GROMACS users Subject: