Re: [gmx-users] Type of unit cell

Have a look at this one: The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions Author(s): Wassenaar, TA (Wassenaar, TA); Mark, AE (Mark, AE) Source: JOURNAL OF COMPUTATIONAL CHEMISTRY Volume: 27 Issue: 3 Pages: 316-325 DOI: 10.1002/jcc

Re: [gmx-users] Velocities in trjconv 4.5.5

--- On Mon, 23/4/12, francesco oteri wrote: > Hi Ignacio,actually .cpt contains velocities and, to extract a .gro > containing them, you can try to use editconf. Thank you, Francesco. editconf doesn't appear to read .cpt files, trjconv does. But my problem is that trjconv does not write veloci

Re: [gmx-users] writing ff parameters as a text file

On Mon, 2012-04-23 at 12:41 -0400, Justin A. Lemkul wrote: > > On 4/23/12 11:36 AM, Bala subramanian wrote: > > Friends, > > I have created the top (attached) file for a tripeptide using pdb2gmx tool > > of > > gromacs. However in the top file, i dnt see the pdb2gmx writing the ff > > parameter

[gmx-users] Chemical potential of protein

Dear Gmx users, Will standart Widom technique to calculate the chemical potential (e.g. for water where we introduce extra water molecule and the interaction energy is compared using integrator: tpi) for the protein in vacuum? So in this case shall I introcuce extra protein and do it as with water

[gmx-users] free energy calculation and g_bar error

Dear gmx-users: I was trying to do a free energy calculation of a charged ligand, according to the paper "Calculation of Absolute Binding Free Energies for Charged Ligands and Effects of Long-Range Electrostatic Interactions ", one of the problems with charged ligands is that the use of a sol

[gmx-users] Error in using gromacs for MD simulation

-- Forwarded message -- From: Rossen Apostolov Date: Mon, Apr 23, 2012 at 11:53 PM Subject: Re: error in using gromacs for MD simulation To: vineetha mandlik Please send your questions to the mailing list gmx-users@gromacs.org. This is the administrative mail. Rossen On 2012

Re: [gmx-users] Chemical potential of protein

Hi, Could you explain what you aim to do in more detail? 24 apr 2012 kl. 11.34 skrev Steven Neumann: > Dear Gmx users, > > Will standart Widom technique to calculate the chemical potential (e.g. for > water where we introduce extra water molecule and the interaction energy is > compared using

Re: [gmx-users] Chemical potential of protein

I want to calculate some thermodynamics property of the protein in vacuum - It can be chemical potential, free energy or surface tension. Just thinkin of something very simple. I want to use this property to coarse grain my protein and develope the force field for it. Would you suggest some easy th

[gmx-users] PBC treatment: need an explanation

Dear gmx-users, I know that this is one of the most frequent subjects in the gmx-users list, however please let me ask you for a direct answer, since it seems to me that this particular question was not treated before. I'm performing MD simulations on a dimeric protein, using a rhombic dodecahedr

[gmx-users] the radius of gyration

Dear Gromacs Specialists, I ran one micelle system and obtained the radius of gyration for this as follows: (g_analyze -f gyrate.xvg -av -ee)    standard   -   cumulants from those of set  average   deviation  sqrt(n-1)   a Gaussian distribition  

[gmx-users] Hypericin dimer affinity

Dear Gromacs users, I set up a simulation of 4 Hypericin molecules for 5 ns. 2 of them formed a dimer. Is there any way to find the dissociation constant Kd  and bond energy  of Hypericin ? Thanks in advance Hovakim-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailm

[gmx-users] -com switch in g_rdf

Using the option '-com' results in a RDF were the reference group is the center of mass (COM) of the first group. -> In a system with pure benzene and using the whole system as a group, this reference point would be somewhere in the middle of the box. And choosing this group twice, would result

R: Re: [gmx-users] g_dist explanation

Thanks for the explanation. I should have used apt values for nstxtcout to get what I want. Thanks again Shilpi Il 23.04.12, "Justin A. Lemkul" ha scritto: > > > On 4/23/12 10:59 AM, Shilpi Chaurasia wrote: > >  Hi Gromacs users, > > > >I am using pull code to separate two units of a protei

Re: [gmx-users] Hypericin dimer affinity

On 4/24/12 7:47 AM, Hovakim Grabski wrote: Dear Gromacs users, I set up a simulation of 4 Hypericin molecules for 5 ns. 2 of them formed a dimer. Is there any way to find the dissociation constant Kd and bond energy of Hypericin ? Umbrella sampling is one method from which you might be able

Re: [gmx-users] PBC treatment: need an explanation

On 4/24/12 6:51 AM, Anna Marabotti wrote: Dear gmx-users, I know that this is one of the most frequent subjects in the gmx-users list, however please let me ask you for a direct answer, since it seems to me that this particular question was not treated before. I'm performing MD simulations on a

[gmx-users] why it is so slow in Blue gene?

hello: I am running a 60,000 atom system with 128 core in a blue gene cluster. and it is only 1ns/day here is the script I used for submitting jobs: # @ job_name = gmx_test # @ class = kdm-large # @ error = gmx_test.err # @ output = gmx_test.out # @ wall_clock_limit = 00:20:00 # @ job_t

Re: [gmx-users] why it is so slow in Blue gene?

On 4/24/12 9:42 AM, Albert wrote: hello: I am running a 60,000 atom system with 128 core in a blue gene cluster. and it is only 1ns/day here is the script I used for submitting jobs: # @ job_name = gmx_test # @ class = kdm-large # @ error = gmx_test.err # @ output = gmx_test.out # @ wall_

Re: [gmx-users] PBC treatment: need an explanation

Hi Anna, If there is a representation in which the units are together, then they're together. Trjconv can't put things together which are, in fact, separated. Cheers, Tsjerk On Tue, Apr 24, 2012 at 12:51 PM, Anna Marabotti wrote: > Dear gmx-users, > I know that this is one of the most frequent

Re: [gmx-users] why it is so slow in Blue gene?

On Tue, 24 Apr 2012 15:42:15 +0200 Albert wrote: > hello: > >I am running a 60,000 atom system with 128 core in a blue gene > cluster. and it is only 1ns/day here is the script I used for You don't give any information what exact system that is (L/P/Q?), if you run single or double pr

RE: [gmx-users] gromacs 4.5.5 on Cygwin

Hi Thanks for your earlier reply: ./configure worked after I set CPPFLAGS and LDFLAGS but I am still not able to install gromacs. I configured using the following command: ./configure --disable-threads --enable-all-static --without-xml It worked without any error messages. I entered make and

[gmx-users] make_ndx: atomname selection

Hi all I'd like to do a selection of atom names such as: a C1 C3 C2 C4 to get an index file with 4 atoms (no other matches in the file) and then use it with g_angle to calculate the dihedral. The problem is that make_ndx does not keep the order of atoms in the resulting index file as they ar

[gmx-users] How to increase the ratio of cell size to constrain length per error message

Dear Gromacs Users, I am using gromacs version is 4.5.3. and running my jobs on single node with 8 cores. I have two different systems which contain about 425000 atoms (protein + Lipid +SOL) one with bound ligand and another one unbound protein. I have successfully reached up to NPT equilibrati

[gmx-users] Re: why it is so slow in Blue gene

> hello: > >   I am running a 60,000 atom system with 128 core in a blue gene > cluster. and it is only 1ns/day here is the script I used for > submitting jobs: > > # @ job_name = gmx_test > # @ class = kdm-large > # @ error = gmx_test.err > # @ output = gmx_test.out > # @ wall_clock_limit = 00

[gmx-users] Potential bug? Different results from different versions of gromacs with cos_acceleration

Dear Gromacs users and developers, I found Gromacs 4.5.5 problematic in NEMD calculations for viscosity. As a simple benchmark, I did some calculations for water (TIP5P) and the results are confusing. I applied two methods for the calculation in 300K, 512 waters: 1. momentum fluctuations, 2. pe

[gmx-users] Position restraint of crystal waters

Hi gmxusers, Hope you are well. I am trying to apply position restraints to my crystal waters (just briefly, 1-2ns) but have been unsuccessful. Taking into account the advice from this thread http://lists.gromacs.org/pipermail/gmx-users/2012-February/068780.html, this was what I had done: sys

[gmx-users] Re: why it is so slow in Blue gene

hello guys: thank you very much for kind reply. I am not sure about the thread version since there is only bigsize version of it. And the administrator told me that I have to use the multiples of 32 in the bg_size parameter. The number specified in "-np" should be 4 times bg_size. Pro

Re: [gmx-users] why it is so slow in Blue gene?

hello: it is blue gene P. And the gromacs is single precision in the cluster. Getting Loaded...And the administrator told me that I have to use the multiples of 32 in the bg_size parameter. The number specified in "-np" should be 4 times bg_size. It is even slower than my own workstation

[gmx-users] Fatal error in popc simulation: Atomtype LC3 not found

Dear gmx users, I want to simulate popc in water. What I have done is: 1.Build the popc.top file using the popc.itp parameters and including gmx.ff, lipid.itp and spce.itp in it as below; ; Include forcefield parameters #include "./gmx.ff/forcefield.itp" ; Include water topology #include "./gmx