Re: [gmx-users] GPU calculation of GROMACS in Windows System

li ming wrote: Hi! all: I am informed in OPENMM website that the OPENMM can accelerate GPU calculation of GROMACS in Windows System. How can I apply this method to my study? Any ideas will be welcomed!!! Probably you can't incorporate it in any conventional MD study. See the supported

[gmx-users] supti mukherjee sent you a Friend Request on Yaari

supti mukherjee wants you to join Yaari! Is supti your friend? a href=http://yaari.com/?controller=useraction=mailregisterfriend=1sign=YaariQEL925DEV186ORZ753TEW655;Yes, supti is my friend!/a a

Re: [gmx-users] Matching atom name and types in OPLS-aa FF

Dear Justin and All: I truly appreciate your clear answer. Since my questions are solved by your explanations, I do not know how I can express my grateful heart. Now I have to ask second step questions. :) It is related to the OPLS-aa bon.itp file. Each section (bonds, angle, diherdal, and

Re: [gmx-users] Matching atom name and types in OPLS-aa FF

On Mar 16, 2009, at 9:34 AM, tree wrote: Dear Justin and All: I truly appreciate your clear answer. Since my questions are solved by your explanations, I do not know how I can express my grateful heart. Now I have to ask second step questions. :) It is related to the OPLS-aa bon.itp

[gmx-users] open positions

Dear all, I would greatly appreciate if you could bring this to the attention of those who might be interested. The computational biomolecular chemistry group at the Max-Planck-Institute for Biophysical Chemistry in Goettingen, Germany, is currently looking for phd students and postdocs, who

Re: [gmx-users] problem with pull direction

Message: 1 Date: Sat, 14 Mar 2009 10:41:46 +0800 From: huifang liu huifangliu1...@gmail.com Subject: [gmx-users] problem with pull direction To: gmx-users@gromacs.org Message-ID: e523c6be0903131941oa428a3eo138323abc8067...@mail.gmail.com Content-Type: text/plain;

RE: [gmx-users] Now there are 16 atoms. Deleted 304 duplicates.

Hi, My guess would be that you used the same residue number for all your 20 repeat units. In that case pdb2gmx find 304 duplicate atoms in a single residue and deletes them. Berk From: xiaowu...@hotmail.com To: gmx-users@gromacs.org Date: Sat, 14 Mar 2009 16:06:07 +0800 Subject: [gmx-users]

[gmx-users] Wrong Shake Tolerance

Dear Gromacs-Users, we have the following problem: after running several hundred nanoseconds of a peptide (Gromos FF 53a6) in spc-water (NpT ensemble), we recognized that the tolerance of shake (all-bonds were constrained) was wrongly adjusted: instead of calculating with shake_tol = 0.0001,

RE: [gmx-users] Wrong Shake Tolerance

Hi, That will depend on what kind of properties you are looking at and how accurate you want them. Have inaccurate constraining will usually lead to energy leaking out of your system. If you use reaction-field this will add energy into the system, probably even more than the constraints leak,

RE: [gmx-users] Wrong Shake Tolerance

Dear Berk, thank you very much for the quick reply. We have used regular reaction-field with cut-offs. The average temperature is not too low but 5K too high (compared with the adjustment of the temperature bath), but it read on the user-list that this behavior is common when using RF. We

[gmx-users] angular removal of COM and domain decomposition

Dears, mdrun complains when I am asking for the angular removal of the COM together with dynamic load balance on (with gmx-4.0.4). It says the combination is not implemented and suggests to use particle decomposition, which is unfortunately much much slower. What would happen if the use

[gmx-users] center of mass

Hello, I am wondering if there is a tool implemented in GROMACS that computes the coordinates of the center of mass of each molecule of a simulation box. Thank you Antonia _ Invite your mail contacts to join your friends list with

Re: [gmx-users] center of mass

On Mar 16, 2009, at 5:51 PM, Antonia V. wrote: Hello, I am wondering if there is a tool implemented in GROMACS that computes the coordinates of the center of mass of each molecule of a simulation box. g_traj -f traj.xtc -com Thank you Antonia Invite your mail contacts to join your

RE: [gmx-users] center of mass

Thank you From: x.peri...@rug.nl To: gmx-users@gromacs.org Subject: Re: [gmx-users] center of mass Date: Mon, 16 Mar 2009 17:56:16 +0100 On Mar 16, 2009, at 5:51 PM, Antonia V. wrote:Hello, I am wondering if there is a tool implemented in GROMACS that computes the coordinates of the center

RE: [gmx-users] angular removal of COM and domain decomposition

From: x.peri...@rug.nl To: gmx-users@gromacs.org Date: Mon, 16 Mar 2009 17:36:49 +0100 Subject: [gmx-users] angular removal of COM and domain decomposition Dears, mdrun complains when I am asking for the angular removal of the COM together with dynamic load balance on (with

RE: [gmx-users] Wrong Shake Tolerance

Hi, That is what I expected, as I wrote in my previous mail. You conformations are probably fine. Berk Date: Mon, 16 Mar 2009 17:13:43 +0100 From: andreas.fr...@ch.tum.de To: gmx-users@gromacs.org; oliver.dem...@ch.tum.de Subject: RE: [gmx-users] Wrong Shake Tolerance CC: Dear Berk,

Re: [gmx-users] no ngmx?

Dr. Barbara Gioffreda wrote: Hello to all, I have installed the latest version of gromacs (4.04) to my new Linux (suse 10,3) and I wanted to start working with it. Everything works well, but I cannot start the ngmx . I looked into the directory /usr/local/gromacs/bin and even there is no

Re: [gmx-users] angular removal of COM and domain decomposition

mdrun complains when I am asking for the angular removal of the COM together with dynamic load balance on (with gmx-4.0.4). It says the combination You mean domain decomposition. Yes, sorry! By imposed I mean that the flags are explicitly changed to do angular removal of COM (remove

RE: [gmx-users] angular removal of COM and domain decomposition

Hi, I think you are lucky. The angular comm code only does not work with DD when molecules are partially over the periodic boundaries. But I guess that in your case molecules will never cross the boundary and therefore the comm code will work as it should. Berk From: x.peri...@rug.nl To:

Re: [gmx-users] angular removal of COM and domain decomposition

Indeed we are lucky then! In the mean field there no periodic boundary, the system is spherical. Thanks. XAvier. On Mar 16, 2009, at 7:05 PM, Berk Hess wrote: Hi, I think you are lucky. The angular comm code only does not work with DD when molecules are partially over the periodic

[gmx-users] FOMMS 2009 2nd Circular

This message (also attached as pdf) contains the second circular for the FOMMS 2009 conference. Some of the new information added since the first circular includes a delayed abstract deadline (March 20), the fee schedule, recipient of the inaugural FOMMS Medal, and details about the Workshop on

[gmx-users] Pull code using two reaction coordinates??

Hello everybody: I am trying to perform some PMF calculations using the pull code with a spring (umbrella sampling) but using two reaction coordinates (E1 and E2) between four different groups (r1,r2,r3 and r4). All the examples and tutorials that I found so far on the web, only mention PMF

[gmx-users] virtual atoms: hydrogens on sugars

Hi, I'm trying to create virtual atoms for the hydrogens in a glycosylated protein, specifically the hydrogens on the sugar. I have three types of hydrogens bound to carbon: CH on ring carbon, CH2 on branched carbon, CH3 methyl group. I also have OH and NH hydrogens. Three questions: 1.

[gmx-users] Pull code using two reaction coordinates??

Hi Rodney, This may be possible if your reference is absolute coordinates. In this case, just use pull group 1 and 2, with the reference group undefined. For more nuanced usage, the problem is that you are only allowed one reference group (and one type of pull code usage) in a given run. I

Re: [gmx-users] Pull code using two reaction coordinates??

Hi Rodney, the other alternative is to define the springs in your topology file. You first need to merge your groups (is part of different molecules) and run the different combination you need by defining them by hand; you can easily write a awk script to generate the different topologies

[gmx-users] g_dipoles

Dear Users, I am trying to obtain the dipole moment of a 40 amino acid residue peptide using g_dipoles. I am getting a huge number (about 700 Debye). I expect it to be around 150 Debye (based on other studies). To make sure it I extracted a shapshot of the structure and obtained the dipolemoment

[gmx-users] non-harmonic position restraints

Dear GROMACS users: I'd like to change the functional form for the position restraints potential from the standard harmonic form to a non-harmonic form, e.g., 4-th in the positional deviations, to be effective only in the case for the large deviations. Could you kindly points me about which

Re: [gmx-users] Matching atom name and types in OPLS-aa FF

Dear Dr. Periole: Thank you for your answer. You meant that the types of potential functions do not have any relations with OPLS-aa (except first (1) case). Those (from 2...) are defined as written the Gromacs manual. Thank you again. Sincerely, Kim On Mon, Mar 16, 2009 at 5:42 PM, XAvier

Re: [gmx-users] Matching atom name and types in OPLS-aa FF

Tree wrote: Dear Dr. Periole: Thank you for your answer. You meant that the types of potential functions do not have any relations with OPLS-aa (except first (1) case). Those (from 2...) are defined as written the Gromacs manual. Table 5.4 defines the different types of intramolecular