[gmx-users] gromacs.org_gmx-users Digest, Vol 133, Issue 146
ha.roozbahany
ha.roozbahany at gmail.com
Mon May 25 12:32:33 CEST 2015
Thanks dear Justin for replying me. I will follow your advice.
Sent from Samsung Mobile
-------- Original message --------
From: gromacs.org_gmx-users-request at maillist.sys.kth.se
Date: 05/23/2015 10:03 PM (GMT+04:30)
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: gromacs.org_gmx-users Digest, Vol 133, Issue 146
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Today's Topics:
1. Re: non-glycosilated protein simulation (Justin Lemkul)
2. Re: first residue in chains warning issue (Justin Lemkul)
3. 1-4 interactions in a small molecule are missing (Lee-Ping Wang)
4. Re: 1-4 interactions in a small molecule are missing
(Mark Abraham)
5. Re: 1-4 interactions in a small molecule are missing
(Lee-Ping Wang)
----------------------------------------------------------------------
Message: 1
Date: Sat, 23 May 2015 11:29:34 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] non-glycosilated protein simulation
Message-ID: <55609CDE.3080909 at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
On 5/23/15 9:16 AM, Homa rooz wrote:
> Can I remove ?carbohydrate part of glycosilated protein from pdb structure
> then run MD by gromos force field?
>
You *can* do anything, but the better question is if you *should* do that. Is
the carbohydrate important for function, stability, etc? Are the dynamics of
the nearby residues important to your study?
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
Message: 2
Date: Sat, 23 May 2015 11:29:48 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] first residue in chains warning issue
Message-ID: <55609CEC.5020700 at vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 5/23/15 6:39 AM, Ming Tang wrote:
> Thanks, Justin
>
> For a stable system, is it true that it can be equilibrated endlessly without error? I got LINCS errors when my protein had been equilibrated for about 50ns. Does this mean that there is some wrong with my system?
>
A stable run should never produce LINCS warnings.
-Justin
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
> Sent: Saturday, 23 May 2015 6:24 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] first residue in chains warning issue
>
>
>
> On 5/22/15 3:39 AM, Ming Tang wrote:
>>
>> Dear Justin,
>>
>> Is there any significant difference between the equilibrated states of the protein equilibrated by NPT with all-bonds constrained and without any constraints?
>> If the difference is quite small, then I can choose constraining bonds to increase time step.
>>
>
> This is generally (read: pretty much always) what people do in biomolecular simulations. The bonds are rarely (read: practically never) excited from their ground state, so constraints are a reasonable approximation. This isn't universal, but it's definitely true in most biological systems at ambient conditions.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
Message: 3
Date: Sat, 23 May 2015 09:44:07 -0700
From: "Lee-Ping Wang" <leeping at stanford.edu>
To: <gmx-users at gromacs.org>
Subject: [gmx-users] 1-4 interactions in a small molecule are missing
Message-ID: <06fd01d09577$afc0cf40$0f426dc0$@stanford.edu>
Content-Type: text/plain; charset="us-ascii"
Hi everyone,
I've been trying to understand an issue I've had with a simple molecule in
Gromacs (just 20 atoms) where gen_pairs=yes, nrexcl=3 and all of the atoms
carry some charge. The system is non-periodic with no cutoff. This is a
minimal test case derived from a more complex system (a lipid bilayer) where
I first saw this issue.
My issue is that there is no "Coulomb-14" or "LJ-14" energy term, and the
potential energy does not depend on my setting of fudgeLJ and fudgeQQ. When
I run gmxdump on my .tpr file, it does not output any LJ14 interactions. It
does print out the value of fudgeQQ but this value doesn't have an effect on
the potential energy.
I thought that this molecule should have some 1-4 interactions because there
are several pairs of atoms that are separated by three bonds, and both atoms
have nonzero charge and LJ parameters. I also wrote a Python script to
calculate the Coulomb and LJ energy just for this system, and I confirmed
that Gromacs was behaving as if fudgeLJ and fudgeQQ were both set to zero.
My example calculations are archived and documented here:
https://dl.dropboxusercontent.com/u/5381783/zerotor_excl3.tar.gz
If someone more experienced with Gromacs could look at my files and explain
how I'm misunderstanding the generation and treatment of 1-4 pairs in
Gromacs, I would highly appreciate it.
Thanks,
- Lee-Ping Wang
------------------------------
Message: 4
Date: Sat, 23 May 2015 16:58:29 +0000
From: Mark Abraham <mark.j.abraham at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] 1-4 interactions in a small molecule are
missing
Message-ID:
<CAMNuMATKbsgqzYKeLAMVcKP9KEpWGxxaGN7jhvhpPpaFXTR-6g at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
nrexcl = 3 means to exclude non-bonded interactions up to 3 bonds away, so
you're getting the "no 1-4 interactions" behaviour for which you
inadvertently asked. So set it to 2 and see how you go.
Mark
On Sat, May 23, 2015 at 6:44 PM Lee-Ping Wang <leeping at stanford.edu> wrote:
> Hi everyone,
>
>
>
> I've been trying to understand an issue I've had with a simple molecule in
> Gromacs (just 20 atoms) where gen_pairs=yes, nrexcl=3 and all of the atoms
> carry some charge. The system is non-periodic with no cutoff. This is a
> minimal test case derived from a more complex system (a lipid bilayer)
> where
> I first saw this issue.
>
>
>
> My issue is that there is no "Coulomb-14" or "LJ-14" energy term, and the
> potential energy does not depend on my setting of fudgeLJ and fudgeQQ.
> When
> I run gmxdump on my .tpr file, it does not output any LJ14 interactions.
> It
> does print out the value of fudgeQQ but this value doesn't have an effect
> on
> the potential energy.
>
>
>
> I thought that this molecule should have some 1-4 interactions because
> there
> are several pairs of atoms that are separated by three bonds, and both
> atoms
> have nonzero charge and LJ parameters. I also wrote a Python script to
> calculate the Coulomb and LJ energy just for this system, and I confirmed
> that Gromacs was behaving as if fudgeLJ and fudgeQQ were both set to zero.
> My example calculations are archived and documented here:
> https://dl.dropboxusercontent.com/u/5381783/zerotor_excl3.tar.gz
>
>
>
> If someone more experienced with Gromacs could look at my files and explain
> how I'm misunderstanding the generation and treatment of 1-4 pairs in
> Gromacs, I would highly appreciate it.
>
>
>
> Thanks,
>
>
>
> - Lee-Ping Wang
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
------------------------------
Message: 5
Date: Sat, 23 May 2015 10:33:52 -0700
From: "Lee-Ping Wang" <leeping at stanford.edu>
To: <gmx-users at gromacs.org>
Subject: Re: [gmx-users] 1-4 interactions in a small molecule are
missing
Message-ID: <071601d0957e$a30f4810$e92dd830$@stanford.edu>
Content-Type: text/plain; charset="us-ascii"
Hi Mark,
Thanks for the explanation, and I tried your suggestion. The energy with
setting "nrexcl = 2" is different from "nrexcl = 3", but changing fudgeLJ
and fudgeQQ does not affect the energy in either case. There are still no
Coulomb-14 and LJ-14 energy terms from g_energy.
I think what's happening is that when I set "nrexcl = 2", Gromacs calculates
the full nonbonded interaction between pairs of atoms separated by 3 bonds,
rather than a "1-4 interaction" which is counted as a different energy term
and is scaled by fudgeLJ and fudgeQQ.
This leads me to conclude that there are no 1-4 pairs created when
gen_pairs=yes in grompp. gen_pairs=yes only generates the pair _parameters_
from the atom types, but not the pairs themselves. There are only 1-4 pairs
when there's a "[ pairs ]" section explicitly defined in the topology file,
which pdb2gmx auto-generates for proteins for example. Is this the expected
behavior?
Thanks,
- Lee-Ping
-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Mark
Abraham
Sent: Saturday, May 23, 2015 9:58 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] 1-4 interactions in a small molecule are missing
Hi,
nrexcl = 3 means to exclude non-bonded interactions up to 3 bonds away, so
you're getting the "no 1-4 interactions" behaviour for which you
inadvertently asked. So set it to 2 and see how you go.
Mark
On Sat, May 23, 2015 at 6:44 PM Lee-Ping Wang <leeping at stanford.edu> wrote:
> Hi everyone,
>
>
>
> I've been trying to understand an issue I've had with a simple
> molecule in Gromacs (just 20 atoms) where gen_pairs=yes, nrexcl=3 and
> all of the atoms carry some charge. The system is non-periodic with
> no cutoff. This is a minimal test case derived from a more complex
> system (a lipid bilayer) where I first saw this issue.
>
>
>
> My issue is that there is no "Coulomb-14" or "LJ-14" energy term, and
> the potential energy does not depend on my setting of fudgeLJ and fudgeQQ.
> When
> I run gmxdump on my .tpr file, it does not output any LJ14 interactions.
> It
> does print out the value of fudgeQQ but this value doesn't have an
> effect on the potential energy.
>
>
>
> I thought that this molecule should have some 1-4 interactions because
> there are several pairs of atoms that are separated by three bonds,
> and both atoms have nonzero charge and LJ parameters. I also wrote a
> Python script to calculate the Coulomb and LJ energy just for this
> system, and I confirmed that Gromacs was behaving as if fudgeLJ and
> fudgeQQ were both set to zero.
> My example calculations are archived and documented here:
> https://dl.dropboxusercontent.com/u/5381783/zerotor_excl3.tar.gz
>
>
>
> If someone more experienced with Gromacs could look at my files and
> explain how I'm misunderstanding the generation and treatment of 1-4
> pairs in Gromacs, I would highly appreciate it.
>
>
>
> Thanks,
>
>
>
> - Lee-Ping Wang
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
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