[gmx-users] Regarding generating topology file.

Dear all, I have got some topology and parameter file for some small organic molecules from swissparam in *.mol2 format. I am trying to generate *.top, *.gro & *.itp files using topolbuild. But I dont know how to do. So can anybody give me a link or some materials related to this. Tha

Re: [gmx-users] Regarding generating topology file.

On 02/08/11, Ravi Kumar Venkatraman wrote: > Dear all, > I have got some topology and parameter file for some small > organic molecules from swissparam in *.mol2 format. I am trying to generate > *.top, *.gro & *.itp files using topolbuild. But I dont know how to do. So > can an

Re: [gmx-users] atom types

Hi Justin Again thanks for the reply. I am not disagreeing with you but If I don't include a [pairs] directive in the topology file (with gen_pairs =yes), then there are no 1-4 LJ nor 1-4 Coulombic energies written in the log file. When I include the [pair s] directive then both types of interacti

Re: [gmx-users] atom types

On 02/08/11, Gavin Melaugh wrote: > Hi Justin > > Again thanks for the reply. I am not disagreeing with you but If I don't > include a [pairs] directive in the topology file (with gen_pairs =yes), > then there are no 1-4 LJ nor 1-4 Coulombic energies written in the log > file. When I include t

Re: [gmx-users] atom types

Hi Mark Thanks for the reply. I am currently reading that section of the manual and, unless I am completely mistaken, it seems to vindicate what I am saying. "Extra Lennard-Jones and electrostatic interactions between pairs of atoms in a molecule can be added in the [pairs] section of a molecule

[gmx-users] Re: a question about order parameter of POPC

There is a bug in g_order. It produces -Scd values that are similar to experimental results and those from other simulations, but they are not correct, at least in the case of unsaturations. Saturated carbons should be correct, if I recall. So no, there is no satisfactory answer until the b

Re: [gmx-users] atom types

On 02/08/11, Gavin Melaugh wrote: > Hi Mark > > > Thanks for the reply. > I am currently reading that section of the manual and, unless I am > completely mistaken, it seems to vindicate what I am saying. > "Extra Lennard-Jones and electrostatic interactions between pairs of > atoms in a molecul

Re: [gmx-users] atom types

Yes I think the example vindicates what I am saying as well. I suppose I the "contradiction" ( I'll call it the point of confusion) you refer to is perhaps when Justin (who is always more than helpful) said that "Charges are irrelevant for generation of pair interactions. Nonbonded pair interactio

Re: [gmx-users] atom types

Gavin Melaugh wrote: Yes I think the example vindicates what I am saying as well. I suppose I the "contradiction" ( I'll call it the point of confusion) you refer to is perhaps when Justin (who is always more than helpful) said that "Charges are irrelevant for generation of pair interactions.

[gmx-users] to clear up the confusion regarding fudge LJ and QQ

Hi Justin and Mark Fudge LJ is only used when gen_pairs =yes. Fudge QQ is used regardless. I suppose a more concise and sensible question is the following: Are the atoms involved in the 1,4 Coulombic interactions specified in the [pairs] directive? If not how else are they generated. Cheers Gavi

Re: [gmx-users] atom types

Hi Justin I see that we may have got our wires crossed from the off. Consider the [pairs] directive, which determines which atoms interact in a 1,4 manner. Consider two atoms listed the [pairs] directive. From the point of the Coulombic interaction between these two atoms I suppose my original q

Re: [gmx-users] atom types

On 02/08/11, Gavin Melaugh wrote: > Hi Justin > > I see that we may have got our wires crossed from the off. > Consider the [pairs] directive, which determines which atoms interact > in a 1,4 manner.  Consider two atoms listed the [pairs] directive. From > the point of the Coulombic interacti

Re: [gmx-users] atom types

I hope this doesn't come across as stupid, or worse insolent. But what is the point in stating the charges in the atom type section then ? Gavin Mark Abraham wrote: > > > On 02/08/11, *Gavin Melaugh * wrote: >> Hi Justin >> >> I see that we may have got our wires crossed from the off. >> Conside

[gmx-users] pair types in FEP calculations

Hi there, Could someone please help to understand the use of function types 3 and 2 in the [pairtypes ] directive in the topology file? I am trying to used it in a free energy calculation but the gromacs manual-4.5.4 in the page 112 is kind of confusing. Thanks in advance, Marcelino -- gmx-us

Re: [gmx-users] atom types

Gavin Melaugh wrote: I hope this doesn't come across as stupid, or worse insolent. But what is the point in stating the charges in the atom type section then ? They're probably a holdover from some earlier Gromacs version (an ancient one) that used those charges somehow, or they were listed

Re: [gmx-users] pair types in FEP calculations

Marcelino Arciniega Castro wrote: Hi there, Could someone please help to understand the use of function types 3 and 2 in the [pairtypes ] directive in the topology file? I am trying to used it in a free energy calculation but the gromacs manual-4.5.4 in the page 112 is kind of confusing.

Re: [gmx-users] atom types

On 02/08/11, Gavin Melaugh wrote: > I hope this doesn't come across as stupid, or worse insolent. But what > is the point in stating the charges in the atom type section then ? > It would make sense for a force field that had a fixed charge for some/all atom types. If any such force fields e

Re: [gmx-users] pair types in FEP calculations

On 02/08/11, Marcelino Arciniega Castro wrote: > Hi there, > > Could someone please help to understand the use of function types 3 and 2 in > the > [pairtypes ] directive in the topology file? > I am trying to used it in a free energy calculation but the gromacs > manual-4.5.4 in the > page

[gmx-users] center of box protein

Dear GMX users, I am trying to center my protein at the center of box using editconf. When I view the same using ngmx, the protein seems to lie outside the box neweditconf -f alapdb.pdb -bt cubic  -o boxpdb.pdb -c -center -0.156 -0.061 0.084 -d 1.5 this one works, but the molecule is shifted.

Re: [gmx-users] center of box protein

nahren manuel wrote: Dear GMX users, I am trying to center my protein at the center of box using editconf. When I view the same using ngmx, the protein seems to lie outside the box neweditconf -f alapdb.pdb -bt cubic -o boxpdb.pdb -c -center -0.156 -0.061 0.084 -d 1.5 The protein appe

Re: [gmx-users] malloc on mac

I have a question about the g-hbond selection . after i typed in the g_hbond , it asked me to choose two groops and i am wondering what is difference between Protein and Protein-H ? Thank you Specify 2 groups to analyze: Group 0 ( System) has 7722 elements Group 1 (Protei

Re: [gmx-users] malloc on mac

Sara baretller wrote: I have a question about the g-hbond selection . after i typed in the g_hbond , it asked me to choose two groops and i am wondering what is difference between Protein and Protein-H ? http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups -Justin Thank

[gmx-users] Heat of Vaporization

Hello, I wanted to know your ideas on calculation of heat of vaporization using a single phase run rather than running two separate simulations for liquid and gas! 1- Two separate simulations for liquid and gas DHvap = - + RT 1a: - <*total* potential of a single chain in vacu > ( bond+angle+

Re: [gmx-users] malloc on mac

does the g_hbond work for course grained file. i tried this command and it gave me nothing but an error it does not matter wich selection On Tue, Aug 2, 2011 at 1:01 PM, Justin A. Lemkul wrote: > > > Sara baretller wrote: > >> I have a question about the g-hbond selection . after i typed in th

Re: [gmx-users] malloc on mac

Sara baretller wrote: does the g_hbond work for course grained file. i tried this command and it gave me nothing but an error it does not matter wich selection If there are no hydrogens, there is nothing for g_hbond to measure. You need an atomistic representation such that D-H-A angle

Re: [gmx-users] malloc on mac

Hi Sara, Since you don't have hydrogens, it's hard to talk about hydrogen bonds according to conventional criteria. Note this has nothing to do with malloc; please start a new thread rather than asking your question in another. Cheers, Tsjerk On Aug 2, 2011 7:56 PM, "Sara baretller" wrote:

Re: [gmx-users] malloc on mac

do you suggest any other way to find the hbond?? is the cut of distance of 3 or less something i can do in this case or not?? thank you On Tue, Aug 2, 2011 at 1:58 PM, Justin A. Lemkul wrote: > > > Sara baretller wrote: > >> >> does the g_hbond work for course grained file. i tried this command

[gmx-users] (no subject)

Hi Justin you mentioned in the past email that i can not use the measure hbond; do you suggest any other way to find the hbond?? thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Su

[gmx-users] Re: coarse grain hydrogen bonding

Tsjerk's message covered this: http://lists.gromacs.org/pipermail/gmx-users/2011-August/063472.html To detect a hydrogen bond in a conventional sense using geometric criteria, you need an atomistic representation. There are tools available to reconstruct atomic positions from CG models, but

[gmx-users] Re: Heat of Vaporization

> > Hello, > > I wanted to know your ideas on calculation of heat of vaporization using a > single phase run rather than running two separate simulations for liquid and > gas! > > 1- Two separate simulations for liquid and gas > > DHvap = - + RT > > 1a: - <*total* potential of a single chain in

[gmx-users] Jarzynski and PMF

Dear All, I have tried to calculate the free energy of binding using Jarzynski equality. I employed the following procedure. --I did force pulling simulations along Z-direction as exemplified in Justin's umbrella sampling simulations. I did 50, 250 and 500 pulling simulations to test the converge

Re: [gmx-users] bug in demux.pl

Dear Email Sender, Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Thursday, August 4, 2011. For all questions about CloudBroker and the CloudBroker Platfo

[gmx-users] bug in demux.pl

Hi, I am not sure if this problem has been solved or discussed before. I found that when I use the demux.pl script it does not read the actual time from the .log file. This is for gromacs-4.0.7. These are few lines from one of the .log file for my replica exchnage simulation. For example in the

[gmx-users] spatial distribution function in a binary solvent mixture

Dear all, I'm working with a binary solvent mixture containing 2000 molecules (1800 type-A + 200 type-B). Both the types of solvent molecules have similar structure (they are both diatomic molecules) except the polarity.I'm trying to calculate sdf of type-B solvent molecules. I followed the

[gmx-users] spatial distribution function in a binary solvent mixture

I think that you have a misconception about what g_spatial does. For a system with many type A and many type B, you need to average over all of one type as the central solute to compute an rdf, and perhaps that is what you want for your sdf. g_spatial, however, does not do any fitting. g_sd

Re: [gmx-users] cannot open file

Taylor Kaplan wrote: Hi Justin, I'm running em.sh file as nohup em.sh &. Below is the code in my em.sh file. mpirun -nolocal -np 8 -machinefile machine mdrun_mpi -nice 0 -v -s etExcited.tpr -o etExcited.trr -c etExcited.gro -e etExcited.edr -g etExcited.log -pd &. I've double checke

Re: [gmx-users] bug in demux.pl

On 3/08/2011 8:19 AM, Swarnendu Tripathi wrote: Hi, I am not sure if this problem has been solved or discussed before. I found that when I use the demux.pl script it does not read the actual time from the .log file. This is for gromacs-4.0.7. It reads the values fine, it ju

Re: [gmx-users] bug in demux.pl

I should have looked at the format when it writes the time but thanks for your help. -Swarnendu On Tue, Aug 2, 2011 at 7:07 PM, Mark Abraham wrote: > On 3/08/2011 8:19 AM, Swarnendu Tripathi wrote: > > Hi, > > I am not sure if this problem has been solved or discussed before. > > I found that w

Re: [gmx-users] spatial distribution function in a binary solvent mixture

Thanks Chris. I presume g_sdf won't be helpful for my system. > I think that you have a misconception about what g_spatial does. For a > system with many type A and many type B, you need to average over all > of one type as the central solute to compute an rdf, and perhaps that > is what you wan

[gmx-users] Problem with temperature and stochastic dynamics in FEP

Hi, I am trying to calculate the solvation free energy using thermodynamic integration(TI) method . I am using gromacs 4.0.7 . But, I am having a problem in getting accurate average temperature . The following is what I did: I found that when doing TI, grompp recommends using 'sd' ( stochast

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

Sanku M wrote: Hi, I am trying to calculate the solvation free energy using thermodynamic integration(TI) method . I am using gromacs 4.0.7 . But, I am having a problem in getting accurate average temperature . The following is what I did: I found that when doing TI, grompp recommends u

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

Hi Justin, I first performed two minimization using steep and l-bfgs as the method on the solvated system for each lambda. Then I ran a 500ps NVT simulation on minimized system ( for each lambda) where essentially same .mdp file was used except the following change: gen-vel

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

Sanku M wrote: Hi Justin, I first performed two minimization using steep and l-bfgs as the method on the solvated system for each lambda. Then I ran a 500ps NVT simulation on minimized system ( for each lambda) where essentially same .mdp file was used except the following change: ge

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

Justin A. Lemkul wrote: Sanku M wrote: Hi Justin, I first performed two minimization using steep and l-bfgs as the method on the solvated system for each lambda. Then I ran a 500ps NVT simulation on minimized system ( for each lambda) where essentially same .mdp file was used except the

[gmx-users] spatial distribution function in a binary solvent mixture

Here's the totally wasteful way for you to get what you want: 1. for each molecule in type A: trjorder everything around that molecule and output only the closest N atoms of type A and the closest M atoms of type B. Ensure that the coordinate order is: your central molecule of type A is fir

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

Hi Justin, So, do you suggest that after minimization, I should generate the velocity at 300K instead ? i.,e for equilibration,should following the set-up? gen-vel = yes >> gen-temp= 300 >> gen-seed= -1 From:

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

Sanku M wrote: Hi Justin, So, do you suggest that after minimization, I should generate the velocity at 300K instead ? i.,e for equilibration,should following the set-up? You should always equilibrate under the desired conditions. Never make sudden changes, or else you're going to dama

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

OKK, But, before, I have tried using md as integrator where I start the initial velocity as 280K ( which makes sense as the minimized configuration is essentially at low temperature) and have used Nose-hoover at 300K and I never had problem in getting the desired 300K after running a short NVT s

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

Sanku M wrote: OKK, But, before, I have tried using md as integrator where I start the initial velocity as 280K ( which makes sense as the minimized configuration is essentially at low temperature) and have used Nose-hoover at 300K and I never had problem in getting the desired 300K after ru

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

On 03/08/11, Sanku M wrote: > > > > > > > OKK, But, before, I have tried using md as integrator where I start the > initial velocity as 280K ( which makes sense as the minimized configuration > is essentially at low temperature) and have used Nose-hoover at 300K and I > never had probl

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

Hi Justin, I did calculate the average temperature using last 2 ns of the 8ns data. It is still same 303K. From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Tue, August 2, 2011 9:55:40 PM Subject: Re: [gmx-users] Problem with temperature

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

Sanku M wrote: Hi Justin, I did calculate the average temperature using last 2 ns of the 8ns data. It is still same 303K. Going back to the original .mdp file, I can see that you're using some incorrect settings. You've set rlist=rvdw even though you're using a shifted potential fo

[gmx-users] Force-field checking options

Hi. I'm fairly new to GROMACS, and I've been using it to run some classical MD simulations. In order to be sure that I'm using the correct force field (I had to add a molecule to CHARMM27), I'm comparing it to another simulation code that I know well, CP2K (using GROMACS 4.5.4 and a recent CVS ve

Re: [gmx-users] Force-field checking options

mcgrath wrote: Hi. I'm fairly new to GROMACS, and I've been using it to run some classical MD simulations. In order to be sure that I'm using the correct force field (I had to add a molecule to CHARMM27), I'm comparing it to another simulation code that I know well, CP2K (using GROMACS 4.5.4

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

Finally, I achieved the desired 300K average temperature using sd integrator . I had to reduce the time step from 0.002 ps to 0.001 ps and then running the NVT could produce 300K as average temperature. Still Not sure why md integrator still could 300K average temperature using 0.002 ps a

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

On 3/08/2011 2:23 PM, Sanku M wrote: Finally, I achieved the desired 300K average temperature using sd integrator . I had to reduce the time step from 0.002 ps to 0.001 ps and then running the NVT could produce 300K as average temperature. Still Not sure why md integrator still could 300K

[gmx-users] Problem of Kinetic Energy

Hi, there, I simulate a simple system of pure water with rigid TIP4P model in NVT at 273K. Why the total kinetic energy, reported from g_energy, is not equal to the sum of the rotational kinetic energy and the translational kinetic energy, which are obtained from g_traj with options of -ekt and -

Re: [gmx-users] Force-field checking options

Hi Justin, thanks for the response. For the big system, the dihederal is still fine, while now the improper, U-B, and nonbonded (CP2K groups all nonbonded, 1-4, and real space Coulomb into the same term) are off by a factor of 2-3. Is there any way to print the energy due to angles in GROMACS? T

Re: [gmx-users] Force-field checking options

On 3/08/2011 3:34 PM, mcgrath wrote: Hi Justin, thanks for the response. For the big system, the dihederal is still fine, while now the improper, U-B, and nonbonded (CP2K groups all nonbonded, 1-4, and real space Coulomb into the same term) are off by a factor of 2-3. Is there any way to print

Re: [gmx-users] Problem of Kinetic Energy

On 3/08/2011 3:25 PM, Size Zheng wrote: Hi, there, I simulate a simple system of pure water with rigid TIP4P model in NVT at 273K. Why the total kinetic energy, reported from g_energy, is not equal to the sum of the rotational kinetic energy and the translational kinetic energy, which are obtai

Re: [gmx-users] Force-field checking options

On 3/08/2011 3:45 PM, Mark Abraham wrote: On 3/08/2011 3:34 PM, mcgrath wrote: Hi Justin, thanks for the response. For the big system, the dihederal is still fine, while now the improper, U-B, and nonbonded (CP2K groups all nonbonded, 1-4, and real space Coulomb into the same term) are off by a