Re: [gmx-users] simulated anealing

2013-12-01 Thread Justin Lemkul
On 12/1/13 2:48 AM, kiana moghaddam wrote: Dear GMX Users I want to run NVT equilibration and NPT equilibration (after NVT) for DNA-ligand interaction and want to increase temperature gradually i.e. from 0 to 300 K over a 100 ps, but i have some questions about this process: when I use

[gmx-users] Umbrella Sampling tutorial

2013-12-01 Thread shahab shariati
Dear Justin Very thanks for your reply I will slow pulling by changing pull_rate1 from 0.01 to 0.001 and pull_k1 from 1000 to 100. I have a basic question. Before minimization, where should I put drug molecule? into water molecules or into lipid bilayer? Should I put drug molecule in the

Re: [gmx-users] simulated anealing

2013-12-01 Thread kiana moghaddam
ِDear Jastin  Thanks your reply. In the first step (NVT equilibration) for heating system by simulated anealing from 0 to 300 K, what is the value of gen-temp? Thanks for your time and consideration. Best Regards Kiana On Sunday, December 1, 2013 4:31 PM, Justin Lemkul jalem...@vt.edu

Re: [gmx-users] Umbrella Sampling tutorial

2013-12-01 Thread Justin Lemkul
On 12/1/13 8:04 AM, shahab shariati wrote: Dear Justin Very thanks for your reply I will slow pulling by changing pull_rate1 from 0.01 to 0.001 and pull_k1 from 1000 to 100. I have a basic question. Before minimization, where should I put drug molecule? into water molecules or into lipid

[gmx-users] gen_seed

2013-12-01 Thread Mahboobeh Eslami
Hi Dear Gmx Users what is the different between gen_seed= -1 and gen_seed=173529? what is the best for NVTequilibration? thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] gen_seed

2013-12-01 Thread Justin Lemkul
On 12/1/13 9:45 AM, Mahboobeh Eslami wrote: Hi Dear Gmx Users what is the different between gen_seed= -1 and gen_seed=173529? From the manual: when gen-seed is set to -1, the seed is calculated from the process ID number. The other is just a default value that has no particular

[gmx-users] Umbrella Sampling tutorial

2013-12-01 Thread shahab shariati
Dear Justin When I placed drug within the lipid bilayer, after Generating Configurations step, I obtained 501 gro files. When I used distance.pl script for these gro files, my summary_distances.dat file is as follows: 00.2756352 10.2535359 20.2447009 30.3004653 40.2936225 5

[gmx-users] Gemcitabine topolgy for OPLS

2013-12-01 Thread Andres Ortega
Hi, i´m trying to run a MD with Gemcitabine using OPLS /AA ff, to get the .itp, should i use topolgen , and then calculate the charges with gaussian ussing ChelpG charges, and replace it, i was wondering if this procedure is correct, algo i´m pretending , to study this molecule with a CNT, and

Re: [gmx-users] Umbrella Sampling tutorial

2013-12-01 Thread Justin Lemkul
On 12/1/13 10:38 AM, shahab shariati wrote: Dear Justin When I placed drug within the lipid bilayer, after Generating Configurations step, I obtained 501 gro files. When I used distance.pl script for these gro files, my summary_distances.dat file is as follows: 00.2756352 10.2535359

Re: [gmx-users] Umbrella Sampling tutorial

2013-12-01 Thread Dr. Vitaly Chaban
The output you got indicates that the pulled group came to the location where it is expected by gromacs to be. The input looks correct, but gromacs' pull code is with surprise inside. I would try to pull in opposite direction, i.e. pull_vec1 = -0 0 1. Turning off barostat during pulling also

[gmx-users] ATB SERVER

2013-12-01 Thread Mahboobeh Eslami
hi my friends I use ATB server for my ligands. which are itp and pdb file used for ligands in md simulation by gromacs. thanks a lot -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] ATB SERVER

2013-12-01 Thread Mark Abraham
There are probably a few tutorials that describe what you're trying to do. Probably none of them are exactly right, but you will learn from doing them regardless. Please do a preliminary search for information before asking questions! :-) Mark On Dec 1, 2013 10:38 PM, Mahboobeh Eslami

[gmx-users] feedback wanted: dropping CUDA 3.2/4.0 support

2013-12-01 Thread Szilárd Páll
Hi, In order to ease the maintenance of the native GPU/acceleration in GROMACS, we are removing support for CUDA versions 3.2 and 4.0 in the next version (5.0). We have two options: - Limit the change to performance impact on the GPU kernels due to the removal of the legacy kernels, but do not

Re: [gmx-users] Invalid order for directive implicit_genborn_params

2013-12-01 Thread Justin Lemkul
On 12/1/13 9:51 PM, rdwducl wrote: Hello, I am trying to use implicit solvation but I am getting the following error from the preprocessor: --- Program grompp_mpi, VERSION 4.6.4 Source code file: