RE: [gmx-users] Is there a way to calculate the hydrodynamic radius using GROMACS?

Hi, There might be a way to do this with Gromacs. But I would think a protein is simply a volume (maybe with one attached water layer) for which there is a simple approximation for the hydrodynamic radius in hydrodynamics. Berk > From: aroberts99...@yahoo.com > To: gmx-users@gromacs.org > Dat

RE: [gmx-users] Re: dihedraltypes funct 4 and 9 in gmx 4.5 amber

Hi, Yes, functiontype 1 and 4 are identical, except that the energy gets added to different terms in the log and energy file. In Gromacs 4.0 (and before) to get a dihedral potential consisting of a sum of cosines with different periodes you could do two things: 1) list multiple proper dihedral

[gmx-users] general Charmm forcefield in gromacs

Hi Does anyone have experience of implementing General Charm force field in gromacs before? Could you please share the files for generating the topologies files (.atp, .itp etc). Thank you Fang -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users P

[gmx-users] Is there a way to calculate the hydrodynamic radius using GROMACS?

Hi, all, I was curious, if there is a way to calculate the hydrodynamic radius of a protein using GROMACS? Much appreciated, Art Dr. Arthur Roberts, Ph.D. University of California, San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences 9500 Gilman Drive #0703 La Jolla, CA 92093-0703

[gmx-users] Re: dihedraltypes funct 4 and 9 in gmx 4.5 amber

Hi Berk and Mark, > Erik was too lazy to document this, I now added it to the manual. > Is this manual available even via git? When funct 4 and 9 appeared? in gmx 4.5? Type 4 is identical to type 1, it is only there to distinguish improper from > proper dihedrals. > So for amber impr. dih. onl

Re: [gmx-users] carbohydrate parameters in ffG53a6

Hi Justin, I compare the few sugars (Glc, Gal, Man), their parameters are indeed nearly identical except for some improper dihedrals. Then I can transfer these parameters to other sugars. How about Glycolipid? For example, the link "phosphatidyl-myo-inositol". Do you have any suggestion? Thanks.

[gmx-users] -e -dt flags

Hi guys, I got a little shocked when I used the -e and -dt in g_hbond, why the default for - e is 0, on manual it says "-e" means "last frame to read from trajectory". I know "-b" means "First frame to read from trajectory" with default 0, why do both default values are the same, and both from

Re: [gmx-users] Speeding up simulation

Large cut-offs can bring artificial artifacts. e.g. *Chemical Physics Letters* Volume 406, Issues 1-3

Re: [gmx-users] Trajectory protonation and inter proton distance calculation

Johannes Beck wrote: Dear GROMACS users, I try to read inter-proton distances from an MD trajectory (GROMACS 4.0.5, ffG53a6) of a peptide. As many distances referring to HAs, HBs etc. are to be evaluated for comparison with NMR distance restraints, I tried to use protonate to add all proton

[gmx-users] Trajectory protonation and inter proton distance calculation

Dear GROMACS users, I try to read inter-proton distances from an MD trajectory (GROMACS 4.0.5, ffG53a6) of a peptide. As many distances referring to HAs, HBs etc. are to be evaluated for comparison with NMR distance restraints, I tried to use protonate to add all protons to the peptide traject

Re: [gmx-users] carbohydrate parameters in ffG53a6

For the sugar parameters you can use Glycam parameters http://glycam.ccrc.uga.edu/documents/gl_params.jsp After with specific script it can be convert to Gromac readable file: http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Other_software I hope it would be usef

Re: [gmx-users] pull code absolute reference

bv07ay wrote: Hello, i am having trouble using the pull options in gromacs 4.0.4. i am simply trying to move a protein from the top of the box to a certain point in the center. i have had no luck using a constant pulling or umbrella pulling the error i receive is: "You are using an absol

Re: [gmx-users] carbohydrate parameters in ffG53a6

Jianhui Tian wrote: Hi Parichita, Thanks for the suggestion. However, the question is what parameters from ffG53a6 can be used for not included sugars or glycolipid. I guess you can not simply use the charge, angle and dihedral values based on the atom types from 53a6. Gromos building b

Re: [gmx-users] carbohydrate parameters in ffG53a6

Hi Parichita, Thanks for the suggestion. However, the question is what parameters from ffG53a6 can be used for not included sugars or glycolipid. I guess you can not simply use the charge, angle and dihedral values based on the atom types from 53a6. Jianhui Date: Wed, 18 Aug 2010 16:18:49 +0530

Re: [gmx-users] Speeding up simulation

That might actually be the best approach speed wise. But it depends on what level of accuracy you wish for your calculations. What is your system like? May be you can have a large cut off but you will have to see what the trade off between speed and accuracy is. On Wed, Aug 18, 2010 at 10:26 AM, m

[gmx-users] pull code absolute reference

Hello, i am having trouble using the pull options in gromacs 4.0.4. i am simply trying to move a protein from the top of the box to a certain point in the center. i have had no luck using a constant pulling or umbrella pulling the error i receive is: "You are using an absolute reference

[gmx-users] help to parse edr file using xdrlib in python

Hi there, I am trying to retrieve energies calculated by gmx in python code. It sounds that I could use xdrlib if only I could understand how gmx data were packed in the edr file. For example, I am doing this: import xdrlib In: f = open('aogAAA.edr').read() In: data = xdrlib.Unpacker(f) In: rep

Re: [gmx-users] Speeding up simulation

On 17/08/10 22:36, Justin A. Lemkul wrote: There is no way to limit PME to certain ranges. It is a method for solving infinite sums. Usually PME is a poor choice for in vacuo simulations and the like, since there's nothing to be done for most of the simulation box. This interests me -I've used

[gmx-users] Electrostatic interaction Vs Z axis

Dear Gromacs users, I want to find the electrostatic interaction energy between ligand and protein, water and ligand during SMD of the ligand through the channel. I have used g_energy but, I need to plot the energy against Z axis of the channel. Could you please help me. Thanks in advance, -- A

[gmx-users] Re: Molecular dynamcis simualtion regarding

Insert another protein and press ENTER... 1. Try energy minimization before MD. 2. Remove constraints temporarily. What will be the result? Dr. Vitaly Chaban > On running, Molecular dynamics simulation of protein-protein complex, While > running md run, i got this error, > * > "Back Off! I

Re: [gmx-users] Molecular dynamcis simualtion regarding

rekkha nivethitha wrote: Hi frnds, On running, Molecular dynamics simulation of protein-protein complex, While running md run, i got this error, * "Back Off! I just backed up complex_pr1.trr to ./#complex_pr1.trr.5# Back Off! I just backed up complex_pr1.edr to ./#complex_pr1.edr.5# Step 0

Re: [gmx-users] carbohydrate parameters in ffG53a6

Hi Jianhui,  For your sugar part you can use PRODRG, which will convert coordinates for small molecules in PDB format (or simple text structures) to the following topology formats: GROMOS, GROMACS and  from literature if you can find out the parameters of ffG53a6 force field,  then you can corre

Re: [gmx-users] reg QM/MM configuring error

vidhya sankar wrote: Dear gmxuser when i try to configure mopac7-1.10 to interface with gromacs . it end in the following error *../lib/cpp sanity check fails* is there is any suggestion to solve this problem ? it would be helpful to me thanks in advance i am expecting yours re T

[gmx-users] Molecular dynamcis simualtion regarding

Hi frnds, On running, Molecular dynamics simulation of protein-protein complex, While running md run, i got this error, * "Back Off! I just backed up complex_pr1.trr to ./#complex_pr1.trr.5# Back Off! I just backed up complex_pr1.edr to ./#complex_pr1.edr.5# Step 0, time 0 (ps) LINCS WARNING r

[gmx-users] An opportunity to test-drive Gromacs on cutting-edge Nvidia GPUs

Hi! We know that some of you have already started to play with the GPU-accelerated version of gromacs-4.5-beta, and that there are more users who have had questions about the strenghts/weaknesses/properties of those gromacs versions. Long-term we're quite committed to CUDA, and it will get sig

[gmx-users] Re: Software to generate polymer coordinates

Dear Dallas: Very useful question, I'm also interested. At the very basic level, GENCONF (gromacs utility) can be used to replicate monomer. One should pay much attention for the size of the elementary box then. The next quest is to force X2TOP to recognize bonds where they are. If you succeed wit