[gmx-users] RE[2]: how to fix molecules and give different temperature

> Do fixed molecules have a temperature? What temperature is in fact? >Yeah, I want to give all fixed molecules a temperature. The >temperature in left box is 253K, in right box is 283K. So there is 30K >gradient between these two boxes. The middle ice should melt from right to >left.

[gmx-users] RE: how to fix molecules and give different

> Thanks for your reply. > > > Do fixed molecules have a temperature? What temperature is in fact? >Yeah, I want to give all fixed molecules a temperature. The >temperature in left box is 253K, in right box is 283K. So there is 30K >gradient between these two boxes. The middle i

[gmx-users] energy groups

Dear Users, I have a question about separating a system into energy groups. In my system, I have a metal atom and a few residues close to the metal atom (catalytic center). I ran the simulation with out any restraints. In the most representative structure, the catalytic center is completely distor

[gmx-users] Force Extension Curve

Hello, Two questions. First, what parameters are to be modified if I want to reduce the output data in the .trr output file in a constraint pull. I am reaching the 4GB allowable maximum and the simulation is shutting down. Second, what command should be used in order to generate a Force Ext

Re: [gmx-users] trjconv pbc membrane

Thanks for the quickly answer. I used 3.3.3 and 3.3.1 version and the lipids of a monocape are above to the other. The lipids are jumping yet after all those changes. I proved each option separately and some combinations of them. trjconv -s a.tpr -f a.xtc -o b.xtc -center trjconv -s a.tpr -f b.xt

[gmx-users]D Gsol from g_sas calculation

Hi to all, I did surface calculation on a protein either with or without Cu-binding, using g_sas with exactly the same parameter setting. For the delta solvation energy from the output file (the the 5th column in the output file with a label of D Gsol), non-Cu bound protein gives all 0, but

RE:[gmx-users] RE: how to fix molecules and give different temperature

Hi Vitaly, Thanks for your reply. Do fixed molecules have a temperature? What temperature is in fact? Yeah, I want to give all fixed molecules a temperature. The temperature in left box is 253K, in right box is 283K. So there is 30K gradient between these two boxes. The

RE: [gmx-users] RE: how to fix molecules and give different temperature

Hi Vitaly, Thanks for your reply. Do fixed molecules have a temperature? What temperature is in fact? Yeah, I want to give all fixed molecules a temperature. The temperature in left box is 253K, in right box is 283K. So there is 30K gradient between these two boxes. The

Re: [gmx-users] About "Invalid order for directive atomtypes"

Justin and Hans, So, as far as I could find, any itp containing [ atomtypes ] has to come first. However, I never dealt with more than one ligand topology itp file. Besides, from the manual, I was expecting that even having others [ atomtypes ] declared in others itp files the last atomtype read

Re: [gmx-users] trjconv pbc membrane

If you use the new version of Gromacs (3.3.3), there are several options that work nicely. Try each of them separately, probably one of them will work, maybe a combination will be necessary based on how much your lipids jump around. trjconv -center (choose DPPC for centering) trjconv -pbc res

[gmx-users] trjconv pbc membrane

Hi: I equilibrated a DPPC membrane that I built. I want to take a snapshot for doing some protein-membrane simulations, but first i have to do somethings for eliminating the lipids out of the box. I have tried with pbc and fit options like people say in the list and it doesn't work. Anybody can he

[gmx-users] Re: Microcanonical MD with PBC

I did try both shifting and switching. Thank you for the reference though, I'll take a good look at it. :) - Lee-Ping ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at ht

[gmx-users] energy groups

Dear Users, I have a question about separating a system into energy groups. In my system, I have a metal atom and a few residues close to the metal atom (catalytic center). I ran the simulation with out any restraints. In the most representative structure, the catalytic center is completely distor

Re: [gmx-users] About "Invalid order for directive atomtypes"

Hans Martin Senn wrote: Hi Alan On 16 Jul 2008, at 18:35, Alan wrote: Hi Hans, Bottom line, when faced this problem, is: #include "ffamber03.itp" ; Include chain topologies #include "topol_A.itp" #include "topol_B.itp" #include "topol_FAD.itp" #include "topol_ZTRP.itp" Always put your lig

Re: [gmx-users] About "Invalid order for directive atomtypes"

Hi Alan On 16 Jul 2008, at 18:35, Alan wrote: Hi Hans, Bottom line, when faced this problem, is: #include "ffamber03.itp" ; Include chain topologies #include "topol_A.itp" #include "topol_B.itp" #include "topol_FAD.itp" #include "topol_ZTRP.itp" Always put your ligand itp right after #includ

[gmx-users] Wilson angle

Hi I want to calculate the wilson angle. but, I am not sure if the wilson angle is the same as the improper dihedral angle. Could anyone tell me this? then , to calculate the wilson angle, use the command, like: g_angle -type improper Thanks Lin ___ g

Re: [gmx-users] About "Invalid order for directive atomtypes"

Hi Hans, Bottom line, when faced this problem, is: > #include "ffamber03.itp" > ; Include chain topologies > #include "topol_A.itp" > #include "topol_B.itp" > #include "topol_FAD.itp" > #include "topol_ZTRP.itp" Always put your ligand itp right after #include "ffamber03.it

[gmx-users] RE: how to fix molecules and give different temperature

> How to give different and fixed temperature to fixed molecules? Do fixed molecules have a temperature? What temperature is in fact? To fix a part of the system in gromacs you should use the key 'comm-grps'. Read the manual, please. To assign different temperatures to different objects you sho

[gmx-users] RE: Using user-tables for simulations in vacuum

>There is no error message except for "segmentation fault". It does the >same thing if I try to energy minimize the system instead of running an MD >simulation. The corresponding mdp file is pasted below: Try to make emstep lower. Check your constraints. Check the potential and its details. When

[gmx-users] RE: Gromacs and restraints

>I will be running protein in explicit water simulations and need a timestep >of 2fs. Forces and energies in the system will be analyzed. What restraint >setup should I choose? I think no critical errors would occur if you use shake or lincs for water in your case.

Re: [gmx-users] About "Invalid order for directive atomtypes" error

Hi Justin On 16 Jul 2008, at 17:50, Justin A. Lemkul wrote: Hans Martin Senn wrote: Hi Xavier On 16 Jul 2008, at 15:51, Xavier Periole wrote: On Wed, 16 Jul 2008 15:04:17 +0100 Hans Martin Senn <[EMAIL PROTECTED]> wrote: Dear all This is a topic that has come up a couple of times here, see,

Re: [gmx-users] Re Re Re: charge group in topology file

[EMAIL PROTECTED] wrote: Thanks for the reply but if you see the charge group which include N and H is not an integer 10 opls_238 2ASN N 3 -0.514.0067 ; qtot 0.5 11 opls_241 2ASN H 30.3 1.008 ; qtot 0.8 24

[gmx-users] Re Re Re: charge group in topology file

Thanks for the reply but if you see the charge group which include N and H is not an integer 10 opls_238 2ASN N 3 -0.514.0067 ; qtot 0.5 11 opls_241 2ASN H 30.3 1.008 ; qtot 0.8 24 opls_238 3ASN

Re: [gmx-users] About "Invalid order for directive atomtypes" error

Hans Martin Senn wrote: Hi Xavier On 16 Jul 2008, at 15:51, Xavier Periole wrote: On Wed, 16 Jul 2008 15:04:17 +0100 Hans Martin Senn <[EMAIL PROTECTED]> wrote: Dear all This is a topic that has come up a couple of times here, see, e.g., http://www.gromacs.org/pipermail/gmx-users/2008-Janua

Re: [gmx-users] About "Invalid order for directive atomtypes" error

On Wed, 16 Jul 2008 17:24:22 +0100 Hans Martin Senn <[EMAIL PROTECTED]> wrote: Hi Xavier On 16 Jul 2008, at 15:51, Xavier Periole wrote: On Wed, 16 Jul 2008 15:04:17 +0100 Hans Martin Senn <[EMAIL PROTECTED]> wrote: Dear all This is a topic that has come up a couple of times here, see, e.g.,

Re: [gmx-users] Atom not found in residue while adding hydrogens

Travis Craddock wrote: The pdb file is of tubulin (1JFF) and the added residue is a methionine residue obtained from (1TUB). The pdb2gmx command line was as follows: pdb2gmx -ff G43a1 -f GDPTUB.pdb -o GDPTUB.gro -p GDPTUB.top where is used the gromacs 96 forcefield. I am currently using gro

Re: [gmx-users] Atom not found in residue while adding hydrogens

The pdb file is of tubulin (1JFF) and the added residue is a methionine residue obtained from (1TUB). The pdb2gmx command line was as follows: pdb2gmx -ff G43a1 -f GDPTUB.pdb -o GDPTUB.gro -p GDPTUB.top where is used the gromacs 96 forcefield. I am currently using gromacs version 3.3.2. The o

Re: [gmx-users] Atom not found in residue while adding hydrogens

Travis Craddock wrote: Hi All, I modified an existing pdb file by adding a missing residue with coordinates obtained from another pdb file of lower resolution. I ran pdb2gmx and received the following fatal error: Atom CA not found in residue MET1 while adding hydrogens Can someone please e

Re: [gmx-users] About "Invalid order for directive atomtypes" error

Hi Xavier On 16 Jul 2008, at 15:51, Xavier Periole wrote: On Wed, 16 Jul 2008 15:04:17 +0100 Hans Martin Senn <[EMAIL PROTECTED]> wrote: Dear all This is a topic that has come up a couple of times here, see, e.g., http://www.gromacs.org/pipermail/gmx-users/2008-January/032114.html . However,

[gmx-users] Atom not found in residue while adding hydrogens

Hi All, I modified an existing pdb file by adding a missing residue with coordinates obtained from another pdb file of lower resolution. I ran pdb2gmx and received the following fatal error: Atom CA not found in residue MET1 while adding hydrogens Can someone please explain this error to me? T

Re: [gmx-users] Using user-tables for simulations in vacuum

Hello, The simulation does not run even for one step and therefore, it is not possible for me to check any of the components such as energy, temperature etc. There is no error message except for "segmentation fault". It does the same thing if I try to energy minimize the system instead of running

[gmx-users] how to fix molecules and give different temperature

Dear users, I want to do a simulation as below configuration: BOX1BOX2BOX3 3 boxes are contacting with their neighbors in x direction. BOX1 and BOX2 are ice crystal, BOX3 is water. I want to fix molecules in BOX1 and BOX3, so they will not move during simulation. And BOX1

[gmx-users] how to fix molecules and give different temperature

Dear users, I want to do a simulation as below configuration: BOX1BOX2BOX3 3 boxes are contacting with their neighbors in x direction. BOX1 and BOX2 are ice crystal, BOX3 is water. I want to fix molecules in BOX1 and BOX3, so they will not move during simulation. And BOX1

Re: [gmx-users] Gromacs and restraints

Hi Matteus, The time step should be smaller than the fastest fluctuations in your system, which are normally X-H bonds, with frequencies around 10fs. To be ten times faster, you should use 1fs, which normally gives stable simulations even if you don't use constraints. If you constrain the X-H bond

Re: [gmx-users] About "Invalid order for directive atomtypes" error

On Wed, 16 Jul 2008 15:04:17 +0100 Hans Martin Senn <[EMAIL PROTECTED]> wrote: Dear all This is a topic that has come up a couple of times here, see, e.g., http://www.gromacs.org/pipermail/gmx-users/2008-January/032114.html . However, despite the recommendations given in that previous post, I

[gmx-users] About "Invalid order for directive atomtypes" error

Dear all This is a topic that has come up a couple of times here, see, e.g., http://www.gromacs.org/pipermail/gmx-users/2008-January/032114.html . However, despite the recommendations given in that previous post, I think the problem is exactly that the information in the manual is not suffic

[gmx-users] Gromacs and restraints

Hi all I´m new to gromacs, having previously worked with Charmm. After looking through articles and gromacs tutorials it seems many use the SETTLE algorithm for water, restraining both water angle and bonds, as well as restraining all bonds in proteins, while using a timestep of 2fs. I believe i

Re: [gmx-users] Using user-tables for simulations in vacuum

sapna sarupria wrote: Hello, Thanks David for your response. Actually I have used the same tables for simulations of the polymer in water and have had no problem with them. Those simulations run for 4 ns without a problem. So the tables are correct and I am sure of that. I am not using the CV

Re: Re: [gmx-users] make_ndx problem

Thanks once again. Ideally I shouldnt do for whole system. Ok. On Wed, 16 Jul 2008 Justin A.Lemkul wrote : > > >minnale wrote: >> but here I am calculating density for 128 lipids not for 64 lipids. Is it >> right what iam doing? > >The examples on the wiki are just a few illustrative ideas, m

Re: [gmx-users] make_ndx problem

minnale wrote: but here I am calculating density for 128 lipids not for 64 lipids. Is it right what iam doing? The examples on the wiki are just a few illustrative ideas, meant to inspire the fact that you can analyze whatever subset of your system you wish. You can certainly analyze all

Re: [gmx-users] Using user-tables for simulations in vacuum

Hello, Thanks David for your response. Actually I have used the same tables for simulations of the polymer in water and have had no problem with them. Those simulations run for 4 ns without a problem. So the tables are correct and I am sure of that. I am not using the CVS version and so I give the

Re: [gmx-users] Using user-tables for simulations in vacuum

sapna sarupria wrote: -- Forwarded message -- From: *sapna sarupria* <[EMAIL PROTECTED] > Date: Tue, Jul 15, 2008 at 9:16 AM Subject: Using user-tables for simulations in vacuum To: Discussion list for GROMACS users >

Re: [gmx-users] make_ndx problem

minnale wrote: Thanks for the reply, may be this is trivial question to you That I know that how to select phosrous atom alone of POPC. Normally people are using only phosphrous atom or PO4 group ? for density calculation ,etc analysis. In one article I found that they have done density ana

Re: [gmx-users] definition of J-couplings in g_chi

Abil Aliev wrote: yes, i already checked gmx_chi.c (see my previous message pasted below), and J_NHa is for proton-proton coupling between N-H and Ca-H protons. The problem is that g_chi outputs a J_NHa value for PRO, where there is no NH proton. Is this a bug? it probably uses the position o

Re: Re: [gmx-users] make_ndx problem

Thanks for the reply, may be this is trivial question to you That I know that how to select phosrous atom alone of POPC. Normally people are using only phosphrous atom or PO4 group ? for density calculation ,etc analysis. In one article I found that they have done density analysis for PO4 group

Re: [gmx-users] make_ndx problem

Hi, On Wednesday, 16. July 2008, minnale wrote: > Hi Users, > I want to do analysis of g_density of lipidbilayer so how can I select po4 > and N(CH3)3 groups seperately by using make_ndx from popc. Can anyone tell > me detail with which options use? > I have checked in archives that create sn1.nd

Re: [gmx-users] make_ndx problem

minnale wrote: Hi Users, I want to do analysis of g_density of lipidbilayer so how can I select po4 and N(CH3)3 groups seperately by using make_ndx from popc. Can anyone tell me detail with which options use? I have checked in archives that create sn1.ndx and sn2.ndx files but i didnt get c

[gmx-users] make_ndx problem

Hi Users, I want to do analysis of g_density of lipidbilayer so how can I select po4 and N(CH3)3 groups seperately by using make_ndx from popc. Can anyone tell me detail with which options use? I have checked in archives that create sn1.ndx and sn2.ndx files but i didnt get celarly. Thanks

[gmx-users] Using user-tables for simulations in vacuum

-- Forwarded message -- From: sapna sarupria <[EMAIL PROTECTED]> Date: Tue, Jul 15, 2008 at 9:16 AM Subject: Using user-tables for simulations in vacuum To: Discussion list for GROMACS users Hello users, I am trying to do a simulation of a polymer chain (which is simply a bead o

[gmx-users] release of GROMACS 4

Dear GROMACS developers, just a simple question for you: when will the new GROMACS version (GROMACS 4) be released? Thank you very much and best regards Anna __ Anna Marabotti, Ph.D. Laboratorio di Bioinformatica e Biologia Computazionale Istituto di

Re: [gmx-users] Still :Partial charges QM to GROMACS

The derivation of Gromos96 parameters started with some QM, but only to get the electron densities, if I remember correctly. The QM charges were never used. The partial charges were assigned to each atom empirically using a reasonable guess based on the electron densities from QM, and adjusted

RE: [gmx-users] definition of J-couplings in g_chi

yes, i already checked gmx_chi.c (see my previous message pasted below), and J_NHa is for proton-proton coupling between N-H and Ca-H protons. The problem is that g_chi outputs a J_NHa value for PRO, where there is no NH proton. Is this a bug? Abil -- Date: Mon, 14 Jul 2008 There

Re: [gmx-users] Diffusion Cofficient of POPC

On Wed, 16 Jul 2008 07:18:17 +0200 Jojart Balazs <[EMAIL PROTECTED]> wrote: Dear Minnale, As far as i know, at least 100ns simulation should be performed in order to obtain the correct diffusion coefficient for lipids. I think, if you performed 5 ns it is too short. I am not sure about that!

[gmx-users] Still :Partial charges QM to GROMACS

Dear Gromacs Users,  I think I did not frame my question correctly tha last time around. Sorry. Lets say for a C-H (alkyl) bond the partial charges ( from SEMI-EMPIRICAL) are (in bracket) C(0.234)-H(0.045) . so when I am using united atom ff such as GROMOS96 should I take the partial charges